Ok, I'm at a loss now. What exactly is the diff file for? Here's what I do:

1) download the free Upgrade
2) Unzip into temp dir
3) Copy all files from temp dir into dir to be upgraded using cp -r * ../dir/
4) run the php upgrade script

I don't think the mysql conversion error is the problem with system because I get a 500 error not a database access error.

Dowloading to my laptop and then moving files from each directory doesn't seem to make a lot of sense since there are MANY directories. see more If it's permissions that's the issue there should be a permission setting script.

So I'm stuck until I get some help. Pretty frustrating guys, and it's not my first rodeo.