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You might want to contact Roush and see if they have any of their engineers that are working on Ford production calibration development at Ford’s Arizona proving grounds in Wittmann, AZ for the winter. Roush does a ton of production calibration work for Ford and more specifically for Ford’s SVT group. These are the same powertrain engineers that work alongside the engine guys who develop the FI for the crate motors. I have witnessed this first hand when I worked for Ford’s SVT group and they were working in our building (owned by Roush) on the 402/427 FI engines. I can PM you the e-mail addresses of some of the folks I use to work with at Roush, they may or may not be able to help you out.

They may be able to help you out in conjunction with their counterparts back in Detroit on a weekend along with your tuner to help get it sorted out. A bad calibration or base wiring issue controlling the FI could have been what damaged the engine in the first place (like washing down the cylinders or running too lean and burning a piston/valve). If you don’t get the calibration ironed out you will only continue to damage the new engine.

Worst case see if you can ship the car to them in Detroit (use Reliable or another carrier Roush recommends) and let them iron it out in their shops.