FWIW, I would proceed one step at a time. You can absolutely trust David, these guys have sold and serviced and rebuilt both Cat and Cummins for literally decades. The first engines I had majored in that shop were DDs in the 1980s. Those 6-71s are probably still out there.

Pull the head and see what's going on.

You can also absolutely trust Tony. He has done MANY repowers with those engines and similar ones, and Cummins engineers always sign off on his work so that the warranty is in effect. If he built you exhaust systems, they are done right.

I don't know if you need to pull the engine entirely. Yet. I don't think you are at that point, but (and I hope not) you might get there. But I would do the head first.