Bxs C15 mods

Hi guys, I’m new here and have been reading a hell of a lot of good info on C15 mods and performance, and I’ve used as much of it as I can on my truck. 2005 W900 BXS C15 (originally set at 475 from the factory) 18 SP 3.36 Rears. Before I bought the truck it was flashed to a 550 and had good power compared to the S60 Detroits I was used to. Since I bought it, I put a Bully Dog programmer on it and promptly blew a headgasket, which ended up being due to the liners dropping. Counterbored, inframed, etc and ate another headgasket. (Still with the Bully Dog) but this time due to IVA failure. Talked to a veteran Cat man and he suggested to delete the iva’s, epoxy the sawcut, to keep the gasket flat but still allow flex, and put IPD 16:1 pistons in, which I did. Kept the twins and BXS cam. Truck ran great but never would accept the Iva delete file. Always derated 3-4 times a day. So we decided to swap to a 6nz ECM. Running a stock 600 file I was told. After that, I had an injector crap out so I swapped to 58’s. But ever since the ECM swap, it seems to have a slight miss almost like air in the fuel. But theres no air. Thats alot of background info but my question is, has anyone had experience with this particular setup that can offer an explanation for the “miss” and subsequent vibration?
Any help appreciated!!
Thanks, Clarke