wrangler pentastar 3.6L stock tune ocasionally throttle limiting.

2012 Wrangler 3.6
Mod: KN filter, thick Throttle adapter
I have 2 weird problems.

1: I pulled out the stock tune. everything is the same from the tune from others, except for exhaust cam phaser 1 being disabled, but in the log it showed quad vvt is working normally.

2. occasionally throttle limiting. When acc pedal is half depressed, throttle only opens very little. MAP, Injpw, RPM, Ign Timing, even VVT are all shaking. I didn't found some pattern of this happening.

Any one have ideas?
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OK figured out problem 1， Just leave it there. there are some inconsistency.
but is that partial throttle limit designed to act like that?