Does anybody do a engine harness clean up? Like remove all the unnecessary plugs and wires when all the emisions are removed.

 

Many people do it, however unless you are performing an engine swap into another vehicle with the stock EFI system, or building a track car, in general I'd advise against it.

You're not really gaining anything by removing the extra wiring, but what you are accomplishing is a fairly large project with will result in harnesses splayed out across your garage floor while you constantly refer to the factory wiring diagrams. There's really minimal benefit in a street car for the effort required.