So following up on this in the unlikely case it's useful for someone in a similar position...
To briefly recap, MT2 coming up with EEP NG on bootup.
I thought it was stuck on this screen but since discovered a few button presses bypasses this screen and the game proceeds to run normally.
I purchased and fitted an AAT28C64B-15PU. It didn't work, same error message appeared. I mashed the controller in frustration and it then displayed the following screen:
I let it do it's thing and after some time the game ran normally. Sadly, a hard power cycle yielded the same EEP NG error being reported by the startup test sequence.
I then refitted the original NEC 28C64 chip, invoked the restoration process and voila, problem solved. It's now working 100%.