Hi Chris,
It's been a while, but good luck with this one. I suspect something on the main board, 1.2V, 1.5V or 3.3V rail missing or 27M uPC crystal failing. Not sure.
Every Pioneer main board I've replaced has brought grief wrt wrong software, new software needing to be uploaded, having to phone Pioneer, etc. And that was for warranty units.
Unless you can spot something simple like an obese cap, I'd take big strides to avoid it...starting to sound like you now.
Bruce