misfire issue

[NITEMARE07]

So here is my issue. To start I have a 07 150 with 5.4L. Mostly stock with the exception that I gutted the cats, installed custom dual exhaust which dumps out the side, k&n air filter along with the gotts air intake mod, and a gryphon programmer. If I put my programmer in tranny mode it does ok. If I put it in tow or bump octane to 93 and go with performance it tends to misfire more so when I am holding my speeed below 45. The only thing I can figure is it is doing this because my vehicle is a flex fuel vehicle(blah) and my tuner isn't set up for that. If so, I am thinking of setting up a date to pay a visit to the shop since I would like a custom tune any way(yay) due to the fact my cats are gutted and I would like optimum power. If I do this im slightly confused on how much cash this will set me back. Im sure you guys get tired of answering questions about pricing on stuff like this from nuts like me so pardon my flash of stupidity. Thanks for any input on the issue and time!