I'll ask the shop to check the gap on my plugs, coils are less than a year old, I double checked them before I sent the car to the tuner but I'll ask them to check this as well. They're thinking its the wiring pin out, upon searching for some answers I think I may have found something. I purchased my harness from wiring specialties roughly two years ago, I found a video on youtube from wiring specialties titled "repinning Jz connector" that was posted a year ago. I contacted them and they said that the video applys to "the first couple of harnesses had ignition pin off by 1 pin. If the car ran, you are all good." I figure it doesnt hurt to check.
I also asked the tuner about just switching out for smart coils, he recommended finding whats causing the issue before switching them out though.
Appreciate the speedy response Geno. @Geno750 where did you get your AEM coil plate from?