Dude, your flashing an auto tune into a manual PCM. Back to basics. Get ford to do a PATS relearn. (forscan is apparently able to do this but I haven't trued) The get an appropriate custom tune to suit the mods and the manual pcm. Or reinstall the original auto pcm and get it setup properly to suit the manual box. Pats (passive anti theft system) had the ability to reduce fuel and timing to limit the carz speed of it thinks it's been stolen, I can't say this is the case but it sounds like it.