ShoobieStomper

Another great tool to use is diffmerge. It'd be right there on your desktop, you highlight two files right click and compare. Super simple. Can even do entire folders at once.
By FAR the most useful tool for me though is Windows Grep. You can highlight your folders and files and search the text contents for any string using a normal search or a regular expression. It will help tons when you have a file path off and you can use a regular expression to show you all filepaths in your files, or if you just need to find where you placed a variable.

Add the following to your mission.sqm under addons :

"warehouse", "mbg_killhouses", "mbg_buildings_3", "mbg_african_buildings", 
The last one on the list can't have a comma.

Tested this out on my server it works.