So I bought the ultimate collection so I didn't have to use my dozen or so CDs for the various C&C games I've collected over the years, and I've never used mods except for one.

The Global Conquest mode on Kane's Wrath had stupid-ass secondary victory conditions so I downloaded a mod to remove them. Well it worked with my CD version, but I cannot for the life of me figure out how to get it to work for the Ultimate Collection. Can anyone explain to me how? I've already re-installed the mod for GC and the "fixed launchers", but beyond that I'm clueless. Thanks for anyone's time.

I made an updated version of the mod. You can get it here:
http://bibber.bplaced.net/downloads/cnc-3-kanes-wrath/military-conquest/ 

To run the mod install it as stated in the readme file and start it using the WrathEd Mod Launcher which you can get here:
http://bibber.bplaced.net/downloads/cnc-3-kanes-wrath/wrathed-mod-launcher/ 

The fixed launchers are required to make it work with the Ultimate Collection but as you said you have them already installed.

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Has anyone told you that you're *censored*ing awesome?