Like you, I couldn't program a new Allegheny; so I called Lionel service to get authorization to open the shell without voiding the warranty. They instructed me to put the request in writing and send it to "talktous@lionel.com" With authorization, I removed the shell and discovered several problems.
The RUN/PGM switch had been installed with one of the three wires under so much tension, it had broken loose. I soldered in a 1 1/2 inch splice and reattached the wire to the empty post on the switch.
The circuit board for another switch (Smoke ON/OFF) was floating loose and hadn't been attached to the switch. This was a simple matter of inserting the board in the switch and bending over a couple of tabs. Before reattaching the shell, I tested the engine on the track and established that all switches were operating properly.
At that point, I noticed that the two marker lights on the front weren't on. After some detective work, I determined that the polarity of one of the four pin plugs had been reversed. I jury rigged a temporary harness which corrected the polarity, and both lights came on. I need a new plug to complete the permanent repair.
All of the above, I did with photographic documentation in case of future issues with warranty.
A diesel shell is far easier to remove than a locomotive casing. If you have experience such that you can remove the shell without leaving any marks or scratches, you could check to see that there are no loose or broken wires, and no detached circuit boards. If you do identify a problem, it's best to notify Lionel service of any intended repair and receive prior authorization.
Doing my own repair was worth it to me to avoid shipping a heavy locomotive with delicate parts round trip. The tradeoff might not be the same on a diesel.
