Having personally wired several different engines into different chassis (302 EFI into 69 Bronco and '66 Mustang; b35 into an e28; ls3 into an e28), it is ridiculous to see this shop's line items. Over 10 years ago, my car was wired by Terry Conners - a 535is with a 745i turbo swap - keeping intact the 745i ecu, which was not common at the time. The wiring was completed in under a day, but that's because Terry is a professional, and knows exactly what wires interface. It doesn't take 30+ hours to wire and engine swap. If someone is learning on the job, that's a different story. The shop could have easily told Alan that "Hey, I've never wired a Links into an e9 with an s38." Gary is right - Alan has been taken for a ride.
Again I think this reinforces what I said. I think that $1,000 to $1,500 is about right for a very nice custom wiring harness. So using your 1-day number, that is $1,000 in labor at $130 / hr. Add in all of the special colored wire, and the factory connections and $1,500 seems about right to me. My point isn't a woulda-could-shoulda retrospective for Alan. He is a DIY guy but ran into some trouble. That is a risk that us DIY'ers take. However, this thread can serve as a learning opportunity for those whom might think that they can pickup a painless wiring kit for $300 and call it a day, or that a custom harness should cost less than $1,000.