Yes - Something IS wrong. The base (stock) tune in your PCM does not "see" your truck properly. Unless Bill wrote a new "stock" tune for you, I cannot see how his "tune" files would have anything to do with this.
How did you get your truck to run in the first place after the engine swap before Bill entered the picture? I may be wrong,. but I'd guess that someone "flashed" a stock tune into that PCM that made it work with the new engine. Then, Bill wrote custom tunes for that flash (hex code).
My "educated" guess is, the stock flash DID NOT include your ABS brakes. So, I'd bet you need a new stock flash. Once you get this, I suspect Bill will have to rewrite your tunes - similar to getting a dealer reflash.
If what I'm saying is plausible, go back to whoever did your stock flash and make him reflash it with the CORRECT stock tune. Make sure you set your truck back to stock first though!
- Jack
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