S60 low power

New member here, wife suggested I post.

2005 Freightliner Columbia 120
Detroit Series 60 (2018 factory reman engine)
Eaton 10 speed
Last 6: U22121
Back in August I was driving in NM and felt something different with the truck, a hesitation or a stutter, and it started blowing heavy black smoke and we had trouble picking up speed and really noticed a loss of power on even the smallest hills.
New injector cups fixed the smoke but it's been to two Freightliner shops and they can't figure out the power loss (even though together they charged me over 18k).

Fuel pump, compression, turbo, fuel check valve, CAC, EGR Vpod all checked. No fuel contamination, fuel lines, and timing good.

Anything we missed?