Acert c13 stumbles when thermostat opens

I got an 07 freightliner columbia with an acert c13 with a kcb serial number. Over the last year it has always stumbled after the thermostat opens in the morning, especially during winter. It's always went away in about 5 minutes until recently. Now, once the thermostat opens, it just stays with me throughout the day. It's fine between 1300 to 1500 rom cruising but is bad between 900 to 1200 rpm especially in 8th, 9th, and 10th gear. Threw a check engine light the other day for about 5 minutes but doesnt show anything on scan. No codes. No codes in over a year, which is strange for a truck like mine. Took it to a few shops and they ran a cutout test and checked fuel pressure and was good. Said they need a code otherwise it's just a guess. I've been told it could be iva's, could be ecm, could be a bad injector, or a bad injector seal. Doesnt use antifreeze or oil. I've replaced the water seperator, fuel filter, air cleaner, ran some killem through the tank, tightened battery cables, and had an overhead done all in the last month. Engine was replaced about 4 years ago by previous owner and new head was installed about a year and a half ago. Also recently had a new exhaust manifold installed. Old one was cracked. I'm stumped. Any advice would be appreciated and I know the acert c13 has problems. I cant buy another truck right now.