I'm Back Into The Mustang Scene With A Rescue Project.

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.
 
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I was told the wiring harness came from the donor car. But I'm not 100% sure at this point.
The previous owner eliminated all smog / emissions and AC. But the wiring harness for these items is still there.
He also cut the airbag sensors and left the wiring and sensors there. I'll have to get this repaired before I can have the car inspected.

As far as the brakes / 5 lug swap go, it's definitely something I want to do eventually. I just didn't want to drop $$$ on that set up right now.

I need to find a tranny guy that can shed some light on my issue and maybe walk me through the repair / adjustment.