Not many areas flaked off. I think I've now checked every trace and did find one bad connection. Patched that but got the same symptom.
All the joints were reflowed anyway. Even with a lot of flux and scrubbing the pins on the IC don't look great, but test okay.
I guess I can try swapping parts from one board to the other but I've probably already sunk more time into this than it's worth. Any other suggestions?
Mine also shows two 'bcom5714' interfaces in the GIGE slot, despite the airport card reporting as a BCM43xx. I suspect these are the two gigabit ethernet ports built-in to the late 2005 models (possibly adapted from the same parts Apple used for the older PCI-X gigabit ethernet add-in cards.) The Bluetooth on mine is definitely a USB device.
(PCIe Slot 3 and 4 are an AJA Kona 3 and Apple Fibre Channel Card, which also account for the '7x4' and 'dxc' slots.)