On Edit:
Downloading the complete game will certainly give you a solid, working base, but for mission building, you'll want version 2. Download the separate version 2 package from the FTP as well, unable all mods with JSGME( is unable a verb?), then delete the version 2 folder from the jsgmemods folder in your game. Extract the fresh version 2 into the jsgmemods folder, enable using JSGME, and you should be good to go.
I was able to do this twice, on two installs, so it fixed stability and bomb bay issues for me.
Best of luck!
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