There is a slight difference in balance between the 3.8 to the 4.1 engines. It has to do with the bigger pistons. If you use the 3.8 flywheel you just rebalance the assembly with the flywheel.
fuzzyGN and I threw together a 4.1 with a Monza 5-speed and later a BW 4-speed in a Vega wagon. I am not sure what he did balance-wise but it ran pretty good for a cheap build. He would have to chime in as per if it was balanced. I can't remember.