Update!
We finally got the customer back in to have the fuel system upgrade done and the tune ammended. We ended up sticking with the stock ECM's OS and going with the traditional MAF based tuning approach.
So here's the results after the fuel system upgrade and re-tune:
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EFI Calibration Services:
HPtuners, SCT, ECUflash, TunerCats, AEM, FAST, Haltech, etc..