Legacy SD40T-2 not running smoothly at all

Not that this will help you much but I did see a video on Youtube of a Lionel RJ Corman SD40T-2 having the same issues.  If your other engines run fine using TMCC it would seem like the issue is with the locomotive.

perhaps one of the many asc techs will chime in like GGG, Marty, GRJ and Alex all good techs with Lionel issues!

you might check the side rods if it is a steam engine for binding, you can take the top off and turn the flywheel by hand and see if it turns freely other wise could be electronic problem or need reset?

There might be a programming issue.

Have you reset the locomotive? 

Andrew

It could be that it's running in momentum setting "L," which is Low momentum with 32 speed steps. Try setting the momentum to "M," which is Low momentum with 100 speed steps.

Check and see if a traction tire is dragging on a brake shoe. Reasonably common. If this is the case, remove the offending tire and see if the problem goes away. If that fixes it, either put on a new tire or replace all the tires with MTH ones, which are thinner. 

A colleague of mine and I just purchased the UP E6s and on one of his powered A units, it was doing the same thing. So we popped the lid and noticed the decoder wheel below the flywheel had flash along the entire perimeter of the wheel.  I have not run my set yet to see if I have the same issue. 

These parts are run out of a multi cavity tool and used across the board, so I am sure this defect will be seen on other locomotives of the same release.

I would pop the lid and see if you are seeing the "reader board sensor" catching on the decoder wheel.

I just took my gorgeous but problematic engine off of the rails and put my Lionel TMCC Berkshire Nickel Plate #779 back on the rails to see if anything went wrong with her. This Berkshire engine went around the tree at the slowest crawl that you can imagine at the steadiest rate you can fathom. I really am upset about this because I turn to trains to forget about my problems. But it seems like every engine I buy over the internet has a problem???