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Is there a way to allow PHP to read those files that the root uploaded or do I have to run a CHGRP before PHP can touch those files? Is there a setting I can change or to regroup PHP?
if you're uploading the files as apache, and php is running from an apache process it seems like they would be the same user (both apache) so permissions shouldn't be an issue.
Anyway, that's a lot of vagueness to say that I think you need to set apache and whatever user is running the php program to be the same 'group'. Look at the users, not the files or the programs.
(the other alternative is that the ftp program that's doing the uploading isn't setting the permissions correctly - I think this would be changed through settings in the ftp program).
Actually, that's not what I would try next. What I would do is have the user upload via something like ftp or similiar, where the program doing the uploading has the correct permissions.