For $29/mo, we provide access to advanced level technicians who will answer your questions on any Macbook board related matter to the best of their knowledge promptly & walk you through how to solve your problem so you can deliver a working board to your customer.
Having spent some time with the scope this is where I am.
- On start up the fan stutters, makes a spin, stops then starts up for approx 6 seconds. PP5V5_S5 drops to 0v for approx 100ms before raising back to 5.5v
- While the system is running for the 6 seconds or so all voltages are rock solid EXCEPT anything GPU/LCD related - but i'm not sure at what point in the start up sequence we would expect to see this enabled
Be sure the BIOS flashed had clean ME region; to avoid any future issue.
I suppose you didn't change serial number with original from back cover; fix checksum of Fsys area in BIOS is required in such case.