I don't quite get what you have. Your BII has an auto tranny and electric T-case, I get that. But the one you bought is a manual tranny and manual T-case?
If that is the case, then I don't see any problems with swapping the manual tranny and manual case into your BII. Personlly I would put in the manual tranny and manual T-case. The trannies tend to go out on you (sounds like yours already has) and the electric T-cases work when they want to, and don't when you need them to. The the manuals, you KNOW they are going to work, no gambling involved.
And as long as both are 2.9's (which they are), I don't see any reason that they won't swap.