You may very possibly (probably) have to have a custom wiring harness made (or do it yourself if you're truly talented) for just the reasons you mention. It is often easier to change things out as an entire system. Maybe take the opportunity to lose the tranny too. Graft in the whole drive-line...modified GM truck...Jeep...whatever, match-ups become less of an issue, and some electrical/electronic gremlins will be avoided. This is the reason, all our "Frankenstein" vehicles are carbureted and ABS less. Getting the ECU to talk to other peoples parts can be frustrating.