Frankazoid

the engine appears to not have a EGR ... I have matched up the the three jumbo connectors and there seem to be some differences there.

The differences between the manifold and body harness concern me - there shouldn't be any real differences on anything that's '95 to '98. They all plug-in without any changes. What difference are you seeing?

The EGR stuff isn't a problem. As long as the harness is configured for an MT car then there should be no EGR flow sensor or function. Even if the engine had them they would be unused for an MT setup. When you put the EJ22 ECU into MT mode it will ignore that input because it assumes it doesn't exist. An EJ25D ECU on the other hand would still be looking for the EGR in MT mode so hopefully you don't have one of those.

Rick