Update. So I put the engine up on blocks and ran it stationary in conventional mode. It ran perfectly, no stuttering at all. I let it run for a while at different speeds, backward and forward. I even put a little resistance on the wheels with my hand and it still ran smooth.
I tried it on the layout again with TMCC and it continued to stutter at slow speeds.
I then replaced the DCDR borad and tried it again. It still ran bad, so I think that rules out the driver board. I wonder if one of the other boards could be causing the problem.