What was wrong with original transmission?
Why did it lock up what failed inside?
If you are on flat ground with trans in Neutral, engine off, can you roll the truck easily?
Is the front drive shaft turning?
And if driving on flat ground when you push the clutch pedal in does it stay rolling or does it seem to slow down faster than it should.
I can't see transfer case issue "burning out" manual trans, you would notice serious power loss and lots of rolling resistance first.
M5OD-R1 failures are usually from low fluid levels, they heat up and bearings go out.
These transmissions use AFT instead of gear oil so it can leak out easier, rubber plugs top back of transmission are main leak point.
I assume the transfer case shifting works OK now
Can all be engaged and disengaged using the electric shift?
You can test 4WD module and motor, read here: Ford Ranger 4WD Control Module