Migration assistant doesn't migrate all user files

I Wanted to do a semi clean install, so I decided to erase everything and install a fresh OS X Yosemite.
i Used migration assistance to only migrate my user account and all its files. Everything seemed to work fine, until I realized I was missing things. Some fonts were not copied over (/User/name/Library/Fonts) and most of my music was not copied over (~/Music/iTunes etc.). The only music that seemed to transfer were ones I purchased from iTunes or imported recently (with the latest iTunes). I got fed up with the entire process and didn't do any more investigation or debugging and am now doing a full restore from time machine. Luckily I have two time machine backups... Can't always assume everything will go correctly (one time machine is stuffed as it was preparing to backup my new installation with lost user files).
has anyone else had the same problems?
As a note I was able to locate those fonts manually on one of the time machine backups but it said the links we broken (they must be aliases) but since I knew the absolute path I could find them. Maybe that's part of the problem? Also I wonder if user permissions (eg ownership) could affect the restore user account process...
Ps: Apple this site ***** on my iPad mini. Fonts are way too small!

I did exactly that
If so, that would have been Setup Assistant, not Migration Assistant. From the sound of it, I'm not so certain that is what you did. They are very similar, but may produce different results. Setup Assistant appears on the first boot of the new Mac. It is generally far more problem free than Migration Assistant. If you select the option to migrate later you get MA. Have you checked to see if you don't now have another User where all your settings now reside. This can be the result of using MA.
If you didn't use SA on the first boot, it might be far less time consuming and aggravating to simply reinstall the OS and the bundled apps. This will produce a brand new option to use SA on the first boot.

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