Okay I feel your pain.
I would double check your permission settings and also look at the file sizes for 0 bytes. The could be a clue to a bad/corrupted file.
I am talking all of the files.
Like I posted before it might be more simple to restore the backup. Get it working and deal with the upgrade on a different folder to test. Since I see your site has been down for this duration.
BTW I have never seen a issue like this upgrading within the 6x version. But from 5x to 6x all kinds of things happen especially when the code was modified.

Blue Man Group
There is no such thing as stupid questions. Just stupid answers