Alright, I throw in the towel. This Whirlwind board has exceeded my expertise despite my best efforts, and limited response to my tech thread. Ideally, I'd love the opportunity to sit down with someone and go through the diagnosis/repair process if someone in the Pittsburgh area is willing (yes I'd still pay you), as I really want to learn. Otherwise, PM me with your price.
I'd hate to go the Rottendog route on a perfectly salvagable MPU board, and pinballpcb hasn't posted an update since January on their website.