2006 cm870 air in injector leakdown test

[CTTOWING]

The original engine had oil in the coolant and right before we pulled it off the road it was overheated due to a blown coolant hose and we found coolant in the oil. Still was running decent otherwise. I already know, I should have purchased a cummings drop in and all cummings parts, lesson learned. I purchased an engine from a remanufacturer out of Colorado that had good reviews. I purchased injectors, turbo, manifold, and oil cooler from {big name trash tuning company}. When we went to start it, the engine barely ran, it was surging erratically and puffing black smoke like over fueling in one or more cylinders. Short version of the story is we had the 6 injectors warrantied with {big name trash tuning company} ones. We replaced the 4 fuel actuators, fuel shut off solenoid, and low pressure fuel pump with cummings parts and repaired harness from a previous repair. At this point truck runs good going down the road except has trouble finding idle and long crank time when starting. We had bubbles in injector leak test on three cylinders. We purchased 3 cummings injectors. Right now they are all in the front bank. Still have air bubbles from cylinder 1. Have checked cam timing and have adjusted the overhead multiple times. I think the issues we have are caused by air intrusion. What else can cause air in injector leak test, Can cracked head, injector cups? Is there a way to diagnose and the isolate problem?