Mods that I am aware of:
2.9" Pulley
ZZP CAI
3in Exhaust
Not sure about the injectors.

I did my plugs because the car was misfiring pretty badly every now and then. Turns out the previous owner didn't torque two! I swapped out the Autolite 3923's with BRK7E's gapped at .035. After that, the car ran fantastic. But after 100 miles of driving on the highway, I started to notice a stutter and what sounded like spark blowout. I gapped down to .033-.032 and there is still a hint of spark blowout, if you were not looking for it you probably wouldn't hear it but I can feel the loss of power as well. Should I keep messing with the plugs or should I start looking somewhere else? I'm probably going to order some OEM coils and swap that out but what else should I look at?

I find it so bizarre that it ran GREAT for 100 miles.

 

Yes close the gap or buy the hi voltage ZZP coils.

 

What did the plugs look like that you pulled out?

 

Not sure how much boost you're running and if you're logging AFR, but keep dropping the gaps until it all goes away. But too rich a mixture can also cause misfire. FYI I have found 0.026-0.028" with copper plugs works great with a high boost LE5 2.4T and LUV 1.4T running 0.76-0.80 Lambdas so low 11's AFR. If the misfire doesn't go away then it might not be the plugs...

 

Running 15 psi, it threw a code yesterday for a misfire on cylinder 2, swapped out the coil and it seems smooth now. Sort of feels its lower on power though still.

 

I ran a 2.9 and eventually 2.8 pulley on my L61 with the stock cassette style 2-coil, wasted spark shitty ignition system and I never had spark blowout misfires and I ran .032 and even .035 to experiment with smoothing out my idle. When I did get misfires it was from my spark plugs fouling from oil consumption through the valve seals. Idk about LSJ COP but I would assume they are stronger than the L61 cassette style.

Do you have any idea what your AFR is?

 

You shouldn't have an issue at 0.035, unless the car is pig rich, or you have engine damage. Figure out what your AFRs are and do a compression and leak down test.