MustangRacing4.6ltr

hello all , my father in laws 07 Shelby is throwing misfiring codes. He has a h.o. whipple system, with independent belt drive for supercharger upgrade with 373 gears and that's it for mods. Hes running about 11 psi on it . Hes had the ford racing tune on it ever since he got it installed by a reputable ford dealership , he never had this problem. Now after getting dyno tuned a few months back, he did gain 40 more rwhp, but now has this code pop up after about 10 miles of driving. Hes had it back at the ford dealership that originally installed several times now. They claim to have checked all plugs , injectors , fuel pressure etc. and they cannot find one thing wrong with anything. They are also blaming the dyno tuners ( the dealership also uses this dyno tuner for their aftermarket supercharger installs). they have sent it back to the dyno tuner twice with them also saying his tune is spot on. Any suggestions of what else to check? Basically they replace a part , clear the code, he drives it 10 miles or so and the codes comes back. Any help would be appreciated as he is getting rather frustrated with this problem. Thanks in advance. He is bringing it to ford dealership tomorrow.

S197GT07

the actual code would be a good thing to give us to start with