Now that I have everything working again, thanks to Jabram, I am on the hunt for some more self-inflicted problems.
Did anyone toy with the analog I/O pins A0 - A5? (AT2560 pins 97-92.)
They don't seem to be connected to anything on this board, and at least A0 is used for battery voltage monitoring from a divider, if I read the code correct.
I'm thinking that it can't be to hard to connect a header to those pins, and get easy access to battery monitoring, LED 1-4 and a buzzer maybe.
(Hope the weather clears soon, so I can stop fixing things until they are broke, and fly instead.