Tuned CM2250 chuffing/missing/popping

[HOLSTTRUCK]

So I've got a cm2250 that I'm trying to figure out whats going on. It has been de-mandated for a few years now. A few months ago the high pressure pump was about ready to fall off, i replaced it with cummins reman. 2 weeks later the turbo started chuffing intermittently with lots of black smoke when pulling over 50% throttle and under 1500rpm. Shortly after this started the ecm was throwing boost pressure sensor codes, checked it all out and the ecm was bad. Installed a freshly tuned used one, that fixed the boost code but not the chuffing. Shortly after that the turbo actuator and vanes in the turbo went bad so it got a Cummins reman turbo. The chuffing was still happening so we checked out the air to air, it was cracked, got it replaced and ran an overhead. Kind of running out of ideas at this point. Any thoughts???

Parts replaced:
high pressure fuel pump
turbo and actuator
#3 injector
ECM
air to air and all boots
throttle position sensor
exhaust backpressure sensor