A suggestion. Get a conventional engine. Williams by Bachmann would be a good choice. Pull the E Unit and replace it with a bridge rectifier. The engine will no longer back up, but it will start and run forward as soon as power is applied. Cheap, reliable, good pullers.
For controls, I'd suggest an inexpensive Programmable Logic Controller. You'll want start/stop buttons or an on/off selector switch so you can enable the system. A single photo eye will suffice to stop the train at the station. To control the track power, I'd suggest a relay with a normally open held closed contact to switch the power to your center rail. All that is left is some programming.
Automation Direct should have everything you need to make this happen.
