Can I use Migration Assistant to migrate certain data from different sources?

I recently had a hard drive failure (which I now blame on the SATA cable because my SSD became corrupted). I have the stock hard drive that originally came with my MacBook Pro, and I have put it in an enclosure so I can use it via USB. When I restored my hard drive using Time Machine, the computer kept going to sleep despite being connected to power. After about 12 hours being stuck at the same spot, I decided to force shut down the computer and then restart the transfer. When the computer booted back up, all (or at least most, and some data I haven't needed lately) was there. I tried to open the Messages app and it would not open. I reinstalled the OS using the option that would allow me to keep my data, which fixed some errors that the system had been giving me. After researching online, I learned that I should remove the file that stores Messages information (I forget what it was called). My Messages now open, but all previous ones were deleted.

When I get the SATA cable fixed, I want to restore from the Time Machine backup because I still don't fully trust the OS on the hard drive I'm using right now. However, I have other files and messages that have been created that I want to transfer. How should I migrate these files without overwriting any data?

When migrating my system I often "abuse" the Migration Assistant to import my files to a dummy user. Then I create a second user and copy only the files I really want to the new user. Once I am done I delete the dummy user. This strategy should also help you to get your files together.

Some other hints that could interest you:

• You can use rsync with the -c command in Terminal to compare files by their checksum. This is a very slow process because every file will be fully read. However, this gives you absolute certainty if two files are identical or not. Using e.g. rsync -anrcv /Volumes/BackupDisk/OSX/Users/me/ /Volumes/OSX/Users/me would print all files that have different checksums, i.e. are potentially corrupted. I sometimes use that when I suspect that a drive has corrupted data.
• You can use caffeinate in Terminal to keep your Mac from sleeping.