I'll be curious to see how whatever was done (what was done?) will work because I am convinced that the issue is with the cabling somewhere. Like I said, I'd pull the whole thing.

We've had bikes come from the factory with incorrect routing and had to redo all of it (and then bill the manufacturer for time and accessories we had to replace). Before a bike hits the floor we go over the factory build in detail. Nothing impresses a customer more than a bike worth a couple grand that won't shift right on the test ride.