Hi Darryl:
I think you are on the right track removing all the old stuff and starting fresh with the railpro.
So far I have only done 2 steam engines, with the controller in the engine, and the battery in the tender (same as in a box car).
I am using standard lipo rc batteries, 14.4 volts or 18.5v, 5000-6000 mah, depending on the engine and space in the tender. In the first two I was able to leave the coal load unscrewed and remove the fake coal to access the battery for swap out.
My next one that I'm working on wont work that way, so I am leaving the tender body unattached to the base and trucks for easy removal to switch out the battery when needed. I don't do onboard charging, I want to be able to swap out and keep running.
I have the battery connector wired to an on/off toggle switch on the bottom of the can, along with a fuse. I found an available switch / fuse combo unit that can be purchased that is designed just for this.