Yes... its a cluster fuck. From what I've gathered so far, it looks like there will have to be some pins that are shuffled between module 3 and 4.
I think before we go any further, it would be wise to have a cost-benefit discussion. I was browsing ebay today and found several M54 wiring harnesses for around 70-80 bucks. How much is it worth to someone to save 70 or 80 dollars by reusing the existing harness?