Is it possible to rebuild the ~/Library folder completely?
Solution 1:
If you log into the Guest account and everything is running as you suspect, simply create a new user (make sure they are an administrator). Log into the new account and then take ownership of the previous user's Documents, Photo's, Music, etc. folders and move them into the new profile. Depending on how many files you have to move this way it is a quick and easy way to "start over." :D
Solution 2:
Yes the process is simple in concept but takes a long time to finish.
- Make a backup of your system and perhaps a perfect image of ~/Library
- Delete files as you feel is best
- Investigate and solve all the broken programs that stored assets in ~/Library as well as settings.
Step 3 repeats quite often and the best way to work on step 3 is unironically, set up a clean new user and troubleshoot / investigate why your broken account doesn't work as expected.
In reality, most programs work fairly well to patch together the files they need in ~/Library and the breakage generally is Apple Loops for Garage band (older versions especially) and keychain / caches of really seldom used passwords that when needed cause frustration and more lost time than any perceived problem that letting thousands of small, probably unused files lie in ~/Library
Solution 3:
Ummm, while there could be damaged files in your ~/Library folder it is more likely to be a damaged preference file. And rebuilding the ENTIRE ~/Library folder would be difficult and time consuming. Possible but a bit of a PITA...
How I would proceed would be to move the contents of the ~/Library/Preferences folder elsewhere (say, to a temp folder on your desktop. then reboot and see how things are behaving.
Once you have determined that the system itself is OK you can start with your Apps. Just launch them one at a time and see how they are doing.
Note that some Apps store serial numbers inside the preference file and you may have to re-register the software to use it.
Oddly enough this is one of the few troubleshooting steps that remains from the Classic Mac O/S.