Something relatively easy would be swapping out the injectors. For a little increase, the 215hp ones would be good, then a little more would be a 300hp injector set, and of course aftermarket ones if that's not enuf. That's the way to get a good gain in power without touching the pump. There's lots of aftermarket support out there for the engine you have. Plus, it's a lot of expense to replace the engine just to gain that little amount(but the 03 & up 5.9s do burn cleaner). The fuel and rpm adjustments wont hurt the pump a bit. Cummins had the 5.9 rated up to 370hp in marine trim.
Str8 piping does help spoolup, and so will fixing the other bends & kinks in the intake. All the back pressure the engine needs is used to drive the turbo. The best result of going non-muffled is to keep EGT down, the noise at the tail pipe is the added bonus
. Double check the little line going from the intake manifold to the top/ rear of the pump, many times that line can get worn thru, and not let the pump work to full power. It's a boost reference signal to the AFC diaphram. You should be seeing about 20-22 pounds of boost.