So I've been poking around pretty much every day trying to figure this problem out and I figured it out.
It's the JB4.
Not the software apparently but the hardware I guess. I was talking with someone else that just installed their JB4 and they noticed a slight jerk but from the sound of it nothing like mine. Mine felt like full on whiplash inducing bucking, like alarmingly so sometimes. I had already flipped some of the bits on and off and tried different mapping including map0. It was still very prominent in map0 so I assumed the JB4 probably wasn't the issue.
After talking to the other person I decided to just pull the whole JB4 out of the car. The bucking stopped completely. I even put the NGK R plugs back in and still the bucking was completely gone. I put the JB4 back in after a round trip to and from work. There is some small jerking when the turbo is kicking in but the bucking in that odd 2nd/3rd gear 3-4k rpm range is gone. One of the plugs must have had a bad connection but they were both snapped firmly into place.
I did one other thing to the JB4 before I unplugged the system which maybe also could have helped, I dunno. My intake is coming in today so the other day I anticipated removing the air box, which is where my JB4 sits, and relocated it to the top of the fuse box. I noticed when I went to move it the case was burning hot, my car had been off for well over an hour with the hood open to cool it down, I couldn't even hold it. Not sure what the operating temperature is for the JB4 but it was incredibly hot. The new location on the fuse box is much cooler. I can handle it right after turning the car off no problem.
So yeah mystery solved I guess. I take back what I said about the NGK R's they seem to be perfectly fine knowing what I know now.
