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...To have more than one mission.lvl mod?
There have been tons of great mods coming out. Episode 2 troops, Aklays on Kashyyk, Naboo Guards, Jedi in the Jedi Temple, the list goes on and on...
The problem is that I can only have one at a time, is there any way around this?

Well, since its only using 1 mission.lvl file, and they'll overwrite the 'last' one, then it won't

You could also make a copy of the SWBF II's executable, open it in an hex-editor, and replace some occurencies like "mission.lvl" to the name of the second one... (Renamed into "missio2.lvl", for sample)
Then, you just have to rename a tweaked "mission.lvl" file into "missio2.lvl", and place it into your "_LVL_PC" directory...

I've tried that a few days ago, Leviathan and it didn't work. But the executable seems to have an option (maybe a commandline parameter) to use different mission files since there's a "mission%s.lvl" in it. (printf function in C replaces %s with another string)

P.S.: If I just forgot to change a value, please send me a working version.

Sorry to contradict you, DF', but I've already succeeded in making another SWBF II's executable calling a custom "missio*.lvl" file... For that, I've just searched the word "mission" in that file, and replaced some of them by the name of my modded one...