So this happened before the new custom tune. Is this car an actual Roush? If so, I would press them for help. If not and I had the custom tune I would go back to stock and have ford do an analysis this way they can hook up their machine to the car and look.
GT350R - 7 lbs/hp per automobile catalog
DH - power to weight ratio - 7.9 lbs/hp per automobile catalog
Mach 1 - Power to weight ratio - 8.1 lbs/hp per automobile catalog