Finding limiters?

I bought a 2006 Chevy c4500 vin dictates it ass an LLY but its an LBZ. It has a dsp5 switch, s300 t4 non vgt turbo, and a inline map sensor module. It wasnt driving to my liking so i had it flashed back to stock with oe calibration. I only have hptuners presently and i don't believe it goes deep enough into the pids to find whats keeping me in some sort of limp/ limit of 2k rpms and not wanting to shift from not reving high enough. Things checked. Pto engaged,fuel pressure, functional maf,map and iat. There were a couple codes that needed to be disabled and parameters adjusted so they wont check for those sensors. I have efi live on the way hoping it will go a little deeper. I purchased a stealth 64 so i can get the exhaust brake function back and still retain performance. What should i be looking for? This is my first diesel, coming from the turbo LS world. I appreciate any direction.

I have not used HPT on a LBZ. Only EFIlive, if you can send me a more detailed build list, your stock file unlocked and a list of PID I can take a look. I have not used the S64 I only tune brakes via VGT vains.

Thanks, i ended up purchasing efi live. Efi live goes much deeper into the ecm than hp does. Thank you.