High resting CPU usage and Idle Wake Ups

The idle wake ups on my MacBook Activity Monitor are staggering. Earlier today I accidentally deleted a macOS folder and emptied the trash. After realizing what I had done, it was too late. Now the idle wake ups on these programs are ridiculously high. Anyone have a high amount of idle wake ups or know how to solve this? Any help, truly, is appreciated.

EtreCheck version: 5.4.8 (5091)
Report generated: 2020-02-01 08:32:58
Download EtreCheck from https://etrecheck.com
Runtime: 1:19
Performance: Excellent
Sandbox: Enabled
Full drive access: Disabled

Problem: Other problem
Description: 
Too many idle wake ups and threads for each action.

Major Issues: None

Minor Issues:
  These issues do not need immediate attention but they may indicate future problems or opportunities for improvement. 
  Limited drive access - More information may be available with Full Drive Access.

Hardware Information:
  MacBook Pro (13-inch, 2018-2019, Four Thunderbolt 3 ports)
  MacBook Pro Model: MacBookPro15,2
  1 2.3 GHz Intel Core i5 (i5-8259U) CPU: 4-core
  8 RAM - Not upgradeable
    BANK 0/ChannelA-DIMM0 - 4 GB LPDDR3 2133  
    BANK 2/ChannelB-DIMM0 - 4 GB LPDDR3 2133  
  Battery: Health = Normal - Cycle count = 164

Video Information:
  Intel Iris Plus Graphics 655 - VRAM: 1536 MB
    Color LCD (built-in) 2880 x 1800

Drives:
  disk0 - APPLE SSD AP0512M 500.28 GB (Solid State - TRIM: Yes) 
  Internal PCI-Express 8.0 GT/s x4 NVM Express
    disk0s1 - EFI [EFI] 315 MB
    disk0s2 [APFS Container] 499.96 GB
      disk1 [APFS Virtual drive] 499.96 GB (Shared by 4 volumes)
        disk1s1 - Macintosh HD (APFS) (Shared - 256.10 GB used)
        disk1s2 - Preboot (APFS) [APFS Preboot] (Shared)
        disk1s3 - Recovery (APFS) [Recovery] (Shared)
        disk1s4 - VM (APFS) [APFS VM] (Shared - 1.07 GB used)

Mounted Volumes:
  disk1s1 - Macintosh HD
    499.96 GB (Shared - 256.10 GB used, 244.07 GB available, 242.07 GB free)
    APFS
    Mount point: /
    Encrypted

  disk1s4 - VM [APFS VM]
    499.96 GB (Shared - 1.07 GB used, 242.07 GB free)
    APFS
    Mount point: /private/var/vm
    Encrypted

Network:
  Interface en7: iPhone
  Interface en0: Wi-Fi
    802.11 a/b/g/n/ac
  Interface en6: Bluetooth PAN
  Interface bridge0: Thunderbolt Bridge

System Software:
  macOS Mojave 10.14.6 (18G103) 
  Time since boot: Less than an hour

Notifications:
  Notifications not available without Full Drive Access.

Security:
  System Status
  Gatekeeper: Enabled
  System Integrity Protection: Enabled

  Antivirus software: Apple

Kernel Extensions:
  /Library/Extensions
    SamsungPortableSSDDriver.kext (1.5.03 - SDK 10.7)
    SamsungPortableSSDDriverX.kext (1.5.09 - SDK 10.12)

System Launch Agents:
  [Not Loaded]  16 Apple tasks
  [Loaded]  177 Apple tasks
  [Running]  107 Apple tasks

System Launch Daemons:
  [Not Loaded]  36 Apple tasks
  [Loaded]  185 Apple tasks
  [Running]  113 Apple tasks

Launch Agents:
  [Loaded] com.paceap.eden.licensed.agent.plist (PACE Anti-Piracy, Inc. - installed 2020-01-08)

Launch Daemons:
  [Running] com.focusrite.ControlServer.plist (Focusrite Audio Engineering Ltd. - installed 2020-01-08)
  [Running] com.paceap.eden.licensed.plist (PACE Anti-Piracy, Inc. - installed 2020-01-08)
  [Loaded] com.piriform.ccleaner.CCleanerAgent.plist (Piriform Ltd - installed 2019-08-28)

User Launch Agents:
  [Running] com.samsung.portablessd.mon.plist (Samsung Electronics - installed 2020-01-30)

User Login Items:
  [Not Loaded] FocusriteControlServer (Focusrite Audio Engineering Ltd. - installed 2020-01-22)
    Modern Login Item
    /Applications/Focusrite Control.app/Contents/Library/LoginItems/FocusriteControlServer.app

Audio Plug-ins:
  AppleTimeSyncAudioClock: 1.0 (Apple - installed 2019-09-20)
  BluetoothAudioPlugIn: 6.0.14 (Apple - installed 2019-09-20)
  AirPlay: 2.0 (Apple - installed 2019-09-20)
  AppleAVBAudio: 760.6 (Apple - installed 2019-09-20)
  BridgeAudioSP: 5.52 (Apple - installed 2019-09-20)
  iSightAudio: 7.7.3 (Apple - installed 2019-09-20)

Time Machine:
  Time Machine information not available without Full Drive Access.

Performance:
  System Load: 1.33 (1 min ago) 1.38 (5 min ago) 1.21 (15 min ago)
  Nominal I/O speed: 5.91 MB/s
  File system: 17.57 seconds
  Write speed: 1684 MB/s
  Read speed: 2936 MB/s

CPU Usage Snapshot:
  Type Overall
  System 2 %
  User 3 %
  Idle 96 %

Top Processes Snapshot by CPU:
  Process (count) CPU (Source - Location)
  Other processes 22.13 % (?)
  EtreCheck 10.53 % (App Store)
  Dock 0.53 % (Apple)
  Activity Monitor 0.42 % (Apple)
  com.apple.WebKit.WebContent (13) 0.20 % (Apple)

Top Processes Snapshot by Memory:
  Process (count) RAM usage (Source - Location)
  EtreCheck 579 MB (App Store)
  com.apple.WebKit.WebContent (13) 202 MB (Apple)
  Safari 124 MB (Apple)
  Activity Monitor 100 MB (Apple)
  com.apple.WebKit.Networking 100 MB (Apple)

Top Processes Snapshot by Network Use:
  Process (count) Input / Output (Source - Location)
  Other processes 162 KB / 3 MB (?)
  com.apple.WebKit.Networking 97 KB / 6 KB (Apple)
  SystemUIServer 0 B / 64 B (Apple)
  mdworker_shared 0 B / 0 B (Apple)
  spindump_agent 0 B / 0 B (Apple)

Virtual Memory Information:
  Physical RAM: 8 GB

  Free RAM: 172 MB
  Used RAM: 4.90 GB
  Cached files: 2.93 GB

  Available RAM: 3.10 GB
  Swap Used: 0 B

Software Installs (past 30 days):
  Install Date Name (Version)
  2020-01-25 Honey (11.6.13)
  2020-01-30 Two notes Sandbox Patch
  2020-01-30 License Support
  2020-01-30 Samsung Portable SSD Software
  2020-01-30 Soundtheory GULLFOSS (1.4.1)
  2020-01-30 EtreCheck (5.4.8)
  2020-01-30 "Malwarebytes for Mac Uninstaller"
  2020-01-31 Bitdefender Virus Scanner (3.15)

Diagnostics Information (past 7-30 days):
  Directory /Library/Logs/DiagnosticReports is not accessible.
  Enable Full Drive Access to see more information.

End of report

I took it to the Apple store today and they erased everything and restored it. The laptop was fine then, no thousands of idle wake ups. However, just now after plugging it in it's back! Thousands of idle wake ups for kernel task and other programs, within seconds. Newest activity monitor:

UPDATE: I have gone into the system log and even I, without knowing anything about this stuff, can see something is awry. I read on another thread that someone had their ubd process sending to a folder that doesn't exist. I feel like this may be my problem, processes trying to go somewhere where they can't. After all, I did accidentally delete an OS X folder that jump started this whole deal. Here's some system log notes, maybe someone can make sense of it:

Feb  1 12:32:21 localhost syslogd[24]: Configuration Notice:
    ASL Module "com.apple.networking.boringssl" sharing output destination "/Library/Logs/CrashReporter" with ASL Module "com.apple.networking.networkextension".
    Output parameters from ASL Module "com.apple.networking.networkextension" override any specified in ASL Module "com.apple.networking.boringssl".
Feb  1 12:32:21 localhost syslogd[24]: Configuration Notice:
    ASL Module "com.apple.clouddocs" claims selected messages.
    Those messages may not appear in standard system log files or in the ASL database.
Feb  1 12:32:13 localhost systemstats_boot[21]: assertion failed: 18G103: libsystemstats.dylib + 33518 [122ABADA-2C70-30A4-95C3-3D9ABC28B1BC]: 0x26
Feb  1 12:32:13 localhost com.apple.xpc.launchd[1]: Rebuilding caches after update...
Feb  1 12:32:21 localhost com.apple.xpc.launchd[1]: assertion failed: 18G103: launchd + 198119 [BBD445B6-FBA9-3A9C-828F-A112F63E2080]: 0x2
Feb  1 12:32:21 localhost com.apple.xpc.launchd[1]: Early boot complete. Continuing system boot.
Feb  1 12:32:21 localhost com.apple.xpc.launchd[1] (com.apple.cmio.AVCAssistant): ThrottleInterval set to zero. You're not that important. Ignoring.
Feb  1 12:32:21 localhost com.apple.xpc.launchd[1] (com.apple.xpc.launchd.domain.system): com.apple.CoreRAID (lint): The HideUntilCheckIn property is an architectural performance issue. Please transition away from it.
Feb  1 12:32:21 localhost com.apple.xpc.launchd[1] (com.apple.diskmanagementd): ThrottleInterval set to zero. You're not that important. Ignoring.
Feb  1 12:32:21 localhost com.apple.xpc.launchd[1] (com.apple.diskmanagementd): The TimeOut key is no longer respected. It never did anything anyway.
Feb  1 12:32:21 localhost com.apple.xpc.launchd[1] (com.apple.syslogd): The HopefullyExitsLast key is no longer respected. Please remove it.
Feb  1 12:32:21 localhost com.apple.xpc.launchd[1] (com.apple.syslogd): Please switch away from OnDemand to KeepAlive.
Feb  1 12:32:21 localhost com.apple.xpc.launchd[1] (com.apple.opendirectoryd): Unknown key for Boolean: BeginTransactionAtShutdown
Feb  1 12:32:21 localhost com.apple.xpc.launchd[1] (com.apple.xpc.launchd.domain.system): com.apple.opendirectoryd (lint): The HideUntilCheckIn property is an architectural performance issue. Please transition away from it.
Feb  1 12:32:21 localhost syslogd[24]: ASL Sender Statistics
Feb  1 12:32:21 localhost com.apple.xpc.launchd[1] (com.apple.bsd.dirhelper): Service only ran for 0 seconds. Pushing respawn out by 10 seconds.
Feb  1 12:32:21 localhost com.apple.xpc.launchd[1] (com.apple.syslogd[24]): Endpoint has been activated through legacy launch(3) APIs. Please switch to XPC or bootstrap_check_in(): com.apple.system.logger
Feb  1 12:32:21 localhost xpcproxy[118]: libcoreservices: _dirhelper_userdir: 529: bootstrap_look_up returned (ipc/send) invalid destination port
Feb  1 12:32:21 localhost xpcproxy[83]: libcoreservices: _dirhelper_userdir: 529: bootstrap_look_up returned (ipc/send) invalid destination port
Feb  1 12:32:21 localhost xpcproxy[66]: libcoreservices: _dirhelper_userdir: 529: bootstrap_look_up returned (ipc/send) invalid destination port
Feb  1 12:32:21 localhost xpcproxy[63]: libcoreservices: _dirhelper_userdir: 529: bootstrap_look_up returned (ipc/send) invalid destination port
Feb  1 12:32:21 localhost xpcproxy[88]: libcoreservices: _dirhelper_userdir: 529: bootstrap_look_up returned (ipc/send) invalid destination port
Feb  1 12:32:21 localhost Installer Progress[53]: Progress UI App Starting
Feb  1 12:32:21 localhost xpcproxy[122]: libcoreservices: _dirhelper_userdir: 529: bootstrap_look_up returned (ipc/send) invalid destination port
Feb  1 12:32:21 localhost com.apple.xpc.launchd[1] (com.apple.xpc.launchd.domain.system): Service "com.apple.ManagedClient.startup" tried to register for endpoint "com.apple.ManagedClient.agent" already registered by owner: com.apple.ManagedClient
Feb  1 12:32:21 localhost xpcproxy[35]: libcoreservices: _dirhelper_userdir: 529: bootstrap_look_up returned (ipc/send) invalid destination port
Feb  1 12:32:21 localhost xpcproxy[68]: libcoreservices: _dirhelper_userdir: 529: bootstrap_look_up returned (ipc/send) invalid destination port
Feb  1 12:32:21 localhost xpcproxy[51]: libcoreservices: _dirhelper_userdir: 529: bootstrap_look_up returned (ipc/send) invalid destination 

Feb  1 18:12:45 Graysons-MacBook-Pro systemstats[51]: DEPRECATED USE in libdispatch client: dispatch source activated with no event handler set; set a breakpoint on _dispatch_bug_deprecated to debug
Feb  1 18:12:45 Graysons-MacBook-Pro com.apple.xpc.launchd[1] (com.apple.xpc.launchd.domain.user.205): com.apple.pluginkit.pkd (lint): Service sets EnableTransactions=false and EnablePressuredExit=true, which makes no sense. Enabling Transactions.
Feb  1 18:12:45 Graysons-MacBook-Pro xpcproxy[191]: libcoreservices: _dirhelper_userdir: 529: bootstrap_look_up returned (ipc/send) invalid destination port
Feb  1 18:12:46 Graysons-MacBook-Pro airportd[176]: DEPRECATED USE in libdispatch client: Setting timer interval to 0 requests a 1ns timer, did you mean FOREVER (a one-shot timer)?; set a breakpoint on _dispatch_bug_deprecated to debug
Feb  1 18:12:46 Graysons-MacBook-Pro airportd[176]: DEPRECATED USE in libdispatch client: dispatch source activated with no event handler set; set a breakpoint on _dispatch_bug_deprecated to debug
Feb  1 18:12:51 Graysons-MacBook-Pro mds[64]: objc[64]: Class MDSObjectToken is implemented in both /System/Library/PrivateFrameworks/SpotlightServerKit.framework/Versions/A/SpotlightServerKit (0x7fffad002de0) and /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/Metadata.framework/Versions/A/Support/mds (0x10654df40). One of the two will be used. Which one is undefined.
Feb  1 18:12:51 Graysons-MacBook-Pro mds[64]: objc[64]: Class MDSToken is implemented in both /System/Library/PrivateFrameworks/SpotlightServerKit.framework/Versions/A/SpotlightServerKit (0x7fffad002d90) and /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/Metadata.framework/Versions/A/Support/mds (0x10654e490). One of the two will be used. Which one is undefined.
Feb  1 18:12:51 Graysons-MacBook-Pro mds[64]: objc[64]: Class MDSReadCopyUpdate is implemented in both /System/Library/PrivateFrameworks/SpotlightServerKit.framework/Versions/A/SpotlightServerKit (0x7fffad002e30) and /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/Metadata.framework/Versions/A/Support/mds (0x10654f020). One of the two will be used. Which one is undefined.

If you have accidentally deleted part of macOS then the best solution to this issue would be to reinstall macOS as there is no way to guarantee recovery short of reinstalling the operating system.

Reinstall macOS

Warning: Before starting you should backup all your data to an external drive, and fully disconnect this before starting.

I am going to provide a high level over view of the step rather than a detailed step-by-step guide as there are plenty of instructions online on how to reinstall macOS and it varies depending on the operating system version used.

1. Reboot your Mac into Recovery Mode by holding down ⌘ + R until you see the loading screen.

2. Choose to reinstall macOS, this should maintain your data and settings.

Once complete the issue should be resolved, if it is not you will need to try an Erase and Install of macOS.

Erase and install macOS

Best practice: You should always have at least two copies of your data, for the above steps you had one on the computer and one backup, for this we're going to be erasing the one on your computer so you should have two external backups for this, just in case!

1. Reboot your Mac into Internet Recovery Mode by holding down ⌘ + ⌥ + R until you see the spinning globe screen.

2. Launch Disk Utility from the "Utilities" menu bar item at the top (ignore the middle window).

3. Use Disk Utility to erase the internal drive, you may on some operating systems need to select "Show All Devices", make sure you choose the one at the top of the tree. You appear to be running Mojave or Catalina so I would suggest you use the "APFS+" format and "GUID" for the parititon table.

4. Quit Disk Utility and use the main installer window to reinstall macOS onto your new partition.