Get either the free winmerge or buy BeyondCompare or another "diff tool".
These load and compare 2 minium files, and highlight the differences.

There is the mod file with changes/additions to the original for the purpose of making the mod work. Then there are Zen Cart changes between versions(only some files) that contain alterations for at least one of several reasons and these changes are normally required to make the version function as expected.

The diff tool allows one to locate and see the differences easier. The best solution is to obtain the same original file that the mod file was created from and compare all 3 so one can tell what was orig , what the mod altered/added and what the current file has. And tell what are changes between the orig and the current and what the mod differences are, and then you can incorporate these mod changes into the current file.

The only hang here is if you uncover that there are lines that were in the orig that the mod changed and they are then again changed in the current. As in this case, the current code is most likely required for porper function and the mod altered code would require a re-write based upon the new/current code.

More difficult if you have several mods and find that there are changes to the same file for more than one mod