2006 5.9L 2500 cummins 4x4 banks package and six gun on fly!

I had p0336 come up with check engine light. Figured it was the crankshaft position sensor like it said. Currently have the banks six gun on my truck and have had it on for 3 years straight. Drove the truck with the check engine light for 2 weeks then replaced it with one from autozone. Cleared code drove truck to work next day and 10 mins down the road boom check engine light same code p0336. Truck starts acting like its loosing power the gains it right back? Never had any starting problems like I have heard I do have brand new duralast battery's. Cleared the code once more after getting home drove it next day and it wouldn't go over 30-40mph 30 mins into my trip! Pulled over truck actually died when I stopped, checked codes has a injector 5 & 2 out it said! Took it to shop after getting it hauled home had injectors replaced all (6) with 60hp overs! Mechanic told me it was electrical failure on injectors mechanically they where fine! All codes was cleared then mechanic drove it 5 miles down the street and boom p0336 come on starts running sluggish so he takes it back to shop. Calls me after to come take a look after searching forums a while and reading about the ac compressor lines touching the wires I checked but saw no frayed electrical tape or anything actually wasn't rubbing! So then after unplugging ac compressor sensor and some connections around there and cleaning them we tried to let her idle and rev it a little. Everything seemed fine p0336 was still on then all of the sudden p0606 comes on INTERNAL ECM FAILURE?? Did I just fry my ECM lost on what to do have taken banks programmer out completely now!

Please help!