I check the Lionel web site and the motor for the Polar express is the same assembly. Gear is part of the motor not offered a separate item. That tells me it has to be an epoxied part or a formed shaft. If it's a formed shaft that means it's a die-cast shaft, thus crap to work with. As for the fly wheel it looks pretty anemic anyway so I doubt if it would be much of a loss.
Considering your greater experience in the in the drive train side of the hobby I will lay back and let you do all the motor leg work. I'm very good at that!