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Ok, so after a bit of nothing we took another look at this board, and specifically the BMON current sense area, because it looked like a bomb exploded. I managed to restore the circuit, a capacitor was missing, 3v3_S0 was not getting to pin5 of U5601 because of blown trace, and there was a high resistance short to ground on 3v3_S0. after restoration of this area the trackpad and keyboard are now working again under OS.
I guess the system was getting a message that too much power was being used or something? Or maybe it's just coincidence, buit it's solved anyway.
Thanks for the assistence with this one.
Duke is torturing you! This problem is bad SPI line to the CPU as often as PPBUS_G3H short to ground on a 3787 is a dead CPU. I have an entire stack of these waiting for CPUs to cost $10-$30, not much that can be done.