I am pretty sure you'll need new motor mounts going from the I6 to the V8. I'd suggest taking the V8 and leaving the rest.
I have a 79 qtrac CJ and this drivetrain design is just different than the rest, making it difficult to swap parts. The trans, case, and axles are all odd so swapping one means swapping the others. I believe the quadratrac-paired TH400 has a different output shaft than all the other TH400s out there, so finding a transfer case besides the qtrac to bolt up to it will be an issue. If you swap in the trans and the qtrac case, then you are going to need to swap the rear axle as well b/c the quadratrac's rear output has a passenger side offset.