For what it's worth, I am on my second MTH motor and it does not behave nicely. First off, I have installed and programmed very succesfully many locomotives with digitrax and mostly Tsunami decoders. So this is not a programming or wiring issue. My first SD70M burned out 2 decoders, the first a Tsunami, then a digitrax. Both were installed by removing the board and hardwiring it. I then removed the motor as it was running very hot unitil it actually burned out running on the bench in DC. I did get a new motor, no thanks to the LHS that I purchased it from, installed it and worked fine, for a couple of months. Then it started stalling, jerky movememts again, so I took the motor out, ran it on the bench again, and sure enough, the motor was binding slightly and running very rough. Even stalling at about 30% throttle. I added a small drop of oil to both shafts and it smoothed out, a bit. I added another drop and it ran even smoother. I actually had to add about 4 drops of oil to get it to spin, somehwhat normally without sounding lilke a cheap drill. Could it be that many of the "percieved" decoder and wiring issues are simply dry motor shafts binding the engine???? With my stats it appears to be 2 for 2, or should that be 0 for 2. We'll see what longer term affects this has as I am putting the locomotive back to work.
Your story begs the question, what kind of motor did you install the 2nd time. A replacement MTH motor or another brand? Years ago I suffered the same kind of stuff with Bachmann motors, til I started replacing them with motors from A-Line. Since then, not a problem.