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