Jerry,
Keith answered your question pretty well in the thread you posted about the board differences. That also explains why (more than likely) the OP had put a board form an MEP-002a into his 003a and it burned up. The board out of the 112a will work, but NOT for very long inside the 003a due to the increased field current. My guess is that the OP had one of the 400 Hz boards inside of his -002a control box. When he put it in the 003a, a little bit into the test run the magic smoke was let out of it. This is the same reason you NEVER want to idle your generator. The VR will pump up the field current to it's maximum to try to get the voltage up, and will eventually burn up the VR.
Up to what RichardR posted, there is really only one regulator board for the 60 Hz MEP-002a and MEP-003a. The other board and part number he posted is for the MEP-112a 400 Hz genny. I would NOT use it in the 003a. You could get by on an 002a, but if you have both generators and do any amount of parts swapping, sooner or later you are going to forget and put that 400 Hz board in the 003a, and it will not be working for a long time.