chown normally starts with the lowest numbered i-node. See this as a unique identifier. The way i-nodes are numbered differ from system to system, even if you use the same installation/distro.
If you want to compare everything manually, open three ssh sessions, one to your working system (system A), two to your corrupted system (system B). Type
on screen of system A and one screen of system B. Compare each and every line. On the second screen of system B, use
chown right_user.right_group <full file name>
to set the owner/group correctly.
Do all this as user 'root'. Be prepared to work on this for about two days, depending how much you installed.