I took the tight hatch and simply sanded it on a flat piece of 400 grit sandpaper until it fit. I used a Sharpie to blacken the sides again and it's as good as new, and it also comes off easily. It doesn't really take much to get a nice fit.
Sadly, I had to send both units back to Lionel for the rotting couplers and other issues, so I'll have to give my new pair the same treatment.