Well dang, why didn't you tell me what it was in to start with? We could have avoided this whole mess! The military can sure conjure up some crazy stuff...
I kinda of agree with just rebuilding the TH350 though, if you already have one. It's a plenty stout transmission, lots of aftermarket stuff, a cooler is a must with any automatic, and no fab work or parts searching is involved. Unless you really need the OD gear, I'd just stick with it.