I would've saved your iTunes somewhere else first to a flash or something even as a different file if necessary before the uninstall...
Malwarebytes would've taken care of those trojans possibly without uninstalling iTunes.
As far as the trojans being in iTunes start up files..someone good just got to them. Also I remember there being an update the other day for iTunes..possibly helped get rid of the trojans in the startup files?
Either way sucks you lost your music.