Alright, here is about the only advice I can leave you with:
Stop being a "nice guy," get your ass back to the guy that built it, and make him figure it out. He did the build. It worked before, it doesn't work now.
This is why you read thread after thread after thread where people always recommend a reputable diesel specific transmission builder. The locals are just too hit and miss, and it sounds like this one is a miss.