Rough idle in gear, returns normal when in neutral

[t4islander]

The truck is an early 99 that I've had since it was about a year old.
I upgraded some components, new injectors, 4" straight exhaust, and turbo while putting in my PHP chip that replaced a DP Tuner that was in there. The reason for these upgrades was primarily driven by the stock turbo coming apart, the housing was leaking so I decided to upgrade, it did not actually fail. Once I got it back together it just has not idled right consistently. Sometimes it will idle fine, thinking its around 750 rpms or somewhere close, when it gets warmed up it will idle rough and at about 1K rpms. If I drop it into 'N' it seems to return to a smooth/normal idle. I've replaced both ICP and IPR already but no real change. This past weekend I changed oil and decided to siphon out the oil from the HPOP and put some fresh stuff in there. Some of the noise seemed to be reduced but that idle problem is still around. I can't figure out where to look so figured I would ask here for any suggestions. Thanks and happy new year!

Edit: I read somewhere in another thread that a touchy pedal can be an indicator of something wrong... at least that is how I interpreted it. My pedal is definitely super touchy, bumpy roads will get me bucking.