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I downloaded the mod tools and put BF2_modtools in my GameData folder

It then prompts me to insert Disk 1, and after I do, I launch the mod tools. Then it goes into the game, only it is windowed and not fullscreen. I'm not sure what to do.

that is exactly what its supposed to do.... that is a debug .exe though, look in the documentation folder and read the "getting started.doc", then read the all of the other docs, then read everything in the FAQ thread before posting again.

I am sorry, I accidentally must have done something, as I only got the assets and a few other files, and I got no documentation. I reinstalled it and now it works.