I've followed the update steps on these pages:

https://docs.zen-cart.com/user/running/backup/
https://docs.zen-cart.com/user/upgra.../#make-backups

The first page of instructions seemed to go well, and the second page is where my question starts.

2. Execution -
This section's where my backup that I pulled, following the instructions, doesn't seem to want to line up with the files that the 2nd page of instructions under "2. Execution" asks me to compare with WinMerge.

Is anyone able to help me find out where I went wrong? I've gone over it several times. It may be noteworthy that Credit Card/ Shipping Modules are acting improper.