Here she is, just not running right

[Chamberpains]

I see you have fault code 2385 @ 256 counts. With your last codes you posted months ago it didn't show that code. But it did show a very similar code 2384 with 4 counts. Go into Cummins Insite and click the "help" menu and go to "fault tree index" and type in the 2 codes if you haven't already ran down troubleshooting these codes. That control module is VERY temperamental and will cause all kinds of running problems and fuel mileage loss, high EGT's, low boost, fuel knocks, weak ir none existant 3rd stage jakes, all kinds of good things with the cm870's. It is an air operated system after the control module so there is no active feed back if the turbo actuator is in the correct commanded position. Meaning if this leaks air or is faulty in any way, the ECM has no idea where the turbo VG ring is.
Im not saying this is the cause of your rough idle, but it may very well solve some issues that are happening that you may not know about and also save your engine from further abuse and for sure a tortured overheated earlier death.
   
Make sure you follow the tree for the signature and ISX cm870. The ISM cm870 an cm570 appear to have electronic actuator's that your engine does not have.

Also clear out all those inactive codes now that you are aware of what they were and you have done extensive repairs. Some of them can be caused by what you've done and some can be from past owners problems he may have fixed. Clear them and monitor if any come back.