Did you replace injector wiring harness under valve covers? They are know for causing all kinds of problems, don't ask me how I know. I have a 05 ACERT with twins with 1.1M, pretty soon to be 1.2M.
Save up for Inframe. It's time no more band-aid. I did alot you are trying and then some. Make sure you get a new water pump You can get a Inframe kit from IPD if you don't have the money for CAT. You have alot going on. An Inframe will solve 99% of the issues.
1 have you changed wire harness for injectors? 2. Have you changed engine harness? 3 have you had an over-head done? 4. Oil sample? 5. Air to air checked for.leaks? 6. Fuel lines from tank replaced? Just a few of the 1%
2,3,and 6. Gonna check air to air and injectors. Next. Though considering converting to a single turbo and do away with all this actuators and etc.
Depending on where you drive, it could be ok to do. If you goto CAT or any Peterbilt shop. You will have issues with service since you are switching to single turbo. Some won't work on your ride. Unless you know what you want done. But figure out where you will have service done, unless you are doing the work.