I keep checking the schematics over and over and I am either missing something stupid every time or there is just nothing else wrong anywhere.
I think it really needs a fresh pair of eyes to look the whole thing over make sure I am not missing something somewhere.
The only thing I can do is check the lib pinouts do actually match the IC pinouts, they look correct in the schematic, but its the only thing I can really think of checking now.
Only thing else, is to scope out every pin on all the main chips, make sure they all switching, and make sure there is no really bad ringing on any of the signals anywhere.. also note that if there is a problem on some pin somewhere, the scope loading may improve issues or make things worse... its really looking for "leads" to start investigating... Currently I am at a loss where to even start looking
