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.