Like the others have said there is not much worth mentioning when it comes to the differences over the years, plus the majority of the ones your likely to run across have been through the rebuild process enough times that they are now mix and match.
If you still want to know the common variables I am aware of include:
multiple variants of the diesel injector / injector holder
At least 3 different starters (2 types listed in the manual, plus the new current production Southern Automotive brand replacement starter)
Some / Many recent rebuild MEP-002a's have control cabinets and voltage regulators from the 400 Hz 10 KW MEP112's, these are functionally identical, but have a couple of small wiring differences, the best guess around here is the army found they had a surplus of new old stock MEP-112a cabinets and started using them when rebuilding MEP-002a's
There are also some minor cosmetic differences in the fuel tanks / caps as well as the exhaust pipes, etc.
Ike