Ok, after reading (and translating) this whole debacle here is where I think we are:
OP has an 86 2.9 auto 4x4 truck with a leaking vacuum modulator, and a 2.3L Lima engine with a 2wd M5OD hanging around.
There is no way to mix and match any of these powertrain assemblies into any working configuration other than the ones they are already in.
To fix your transmission fluid in the intake issue replace the vacuum modulator on the right rear corner of the transmission, like Floored said to do. As Sno pointed out they are dirt cheap, last one I got was about $20. A failed modulator will effect the 1/2 shift performance of your trans, which can mimic any number of drivability issues. Additionally, and I know this sounds crazy, but gas engines don't really love to run tranny fluid as fuel. They prefer gasoline, and so getting ATF into the intake can cause it's own set of issues, like fouled plugs, if you are sucking up enough. Also, automatics get fussy when they get low on fluid, and that can look like lots of different issues to the untrained observer.
To do your 4-cyl 4x4 swap you would need, at minimum, the output shaft and extension housing from a 4x4 M5OD, in addition to the parts that you already have. Then you would have to tear the transmission completely apart (This will require several unusual tools to be obtained or fabricated, and a shop press since the gears need to be pressed on and of the main shaft that you are replacing). Plus wiring and computers which you already seem to know about.
To put the 2.3 and 2wd trans in as they are now and drive away can be done, but you need the correct rear driveshaft, your existing one is meant to connect to the bolt-up style flange at the rear of a transfer case, and your 2wd trans is designed to accept a slip yoke.
Most of this information is already sprinkled through this thread, I'm just getting it all into one place.