I believe anyone with the funds can do a custom run with Lionel. Lionel's made in the USA boxcar is based on the 9700 series MPC era boxcar. The minimum run is 100 units but is more expensive per unit than the 500 car run from China. It's been a few years since I was TCA's Convention Car Committee chair, so I can't speak to prices, but I do know the graphics are inkjet printed on the car for the Made in USA ones. You can do any custom graphics you like and their graphics department will assist, but Lionel does require written permission to use copyrighted material.
Lionel has a person responsible for club runs, I don't know who that person is these days. For MTH you would contact Andy Edleman. Walter at RMT has offered to help. It would be worthwhile talking to all the companies doing custom runs and see what they can do for you.
