I skipped around and read a few of your posts. What you are doing is similar to what I am going through with my Daddywagon. It started as a 5.0, 5 speed swap from a donor car and evolved into a major bolt on build. I used the ford aftermarket wiring harness. This harness maintains egr function but eliminates the other two exhaust emissions functions, which eliminates the need for the smog pump. I am not familiar with a 4cyl to V8 swap so I don't know how the harnesses interface with one another. But the engine harness itself should be prettymuch a standalone system.