Couple things, "aggressive" tunes wont cause the issues you have.
You took a modded car to a dealership for diagnosing, of course they're gonna blame everything on mods, they're stupid. I still doubt you swapped the tuned ecu with a stock ecu to verify the tune/ecu was causing the issue. You made multiple threads and people tried to help you each time but you continually ignored it and instead kept placing the blame on Jay. I mean honestly, its a ****ing canned tune dude, and you said you had S1 so its not even aggressive, the file on your ecu is likely the same tune file on 200 other BK1 3.8's, so if you were having issues, its something else. You've asked Jay to "turn down the aggressiveness"; wtf do you want Jay to do with a S1 tune to make it less "aggressive"? Anything less than S1 is called stock.
You then tried to fix it by swapping cam sensors, which, you say fixed it for 7k miles then came back. Uhh, thats called "misdiagnosis". And guess what, if the ECU was causing it, it would've happened again by 0.7 miles, not 7,000 of them. Typically if there is something wrong with how an ECU senses and reacts to a condition, it finds its same issue within a few miles. If this got you 7k until your issue came back, you were on the right track but the wrong part.
I bet the next owner has it fixed in a week after he swaps out/regaps plugs and/or finds his dead coil, or intake leak, or the 20 other things that could be causing it before the tune could.
Based on your posts, I know you don't have a 600hp 88 foxbody. Someone who has to ask if the dealer should perform the injector cleaning service and that continually places blame for a simple misfire on the tune doesn't have the where-with-all or patience to build a 600hp anything. Whatever happened to your awesome BC Stroker Kit and going turbo? C'mon, someone that gets this butthurt about a simple misfire and quits, doesn't have or didn't have the ability to make a 600hp car. My 03 Cobra had 450hp/tq through a pulley swap & tune setup and there were days I wish a misfire was the least of my worries.
Which leads me to my next, if you are one of those guys that pays shops and dealers for work, good ****ing luck not getting hosed with that Mustang. I don't know how many local mustang guys I've meet in my days as a mustang owner who have all their **** done at some shop, and then you drive it and its a complete janky POS, hanging throttle, spiky powerband, ultra-lean AFR because the shop is using your wallet for their HP advertisement, so they can claim they make 10hp peak more than the next guy and good luck to you when your
#8 piston melts at 145mph in 5th gear because they tuned it actually super aggressive. Are you going to be there to tell said tuner you only want xx* of max timing at WOT and 11.5:1 AFR max? Or just let him do "his thing"?
Crazy to me, you will hate on Jay who is one of two outfits in the world that tunes these cars, and has probably tuned over 1000+ gen coupes (half of those probably in person), but you'll trust Fred at "Fast Mustangs R Us" down the street from you that might be on his 10th S550 GT? Good ****ing luck with that.