fuel pressure/ timing and quantity

On one of the modules, he said he made some minor adjustments for the bigger 10mm cp3 pump. what, how, and where to make those adjustments? I have a Cummins 2003 H/O. reentrant pistons (closed bowl) design. I now have 150% over injectors with a 12mm cp3 pump. My last engine I had three cracked pistons and suspected bad tune. this new engine has the new fuel system as stated above. ported heads with larger valves. stage3 colt cam. compound turbos 64/71/12 over s480. chamfered and coated pistons with Carrillo rods. all studded with gorilla girdle. Bunch of money to say the least. I just don't want to damage the new engine. I am not looking to put it at max power but useable power for towing as well. The directions stated on the cp3 pump says I have to make adjustments but that is it. I purchased these lessons to do it myself but there's a lot of pids not covered IE "main pulse limiter, main pulse type, start angle correction. voltage to pressure conversion, engine friction fuel quantity. and so on. I have an injector flow chart, but don't really know how to translate that to the program. I am using HP tuners.. Any kind of help would be much appreciated. I do have egt temps on front and rear bank, as well as post turbos, exhaust pressure sensor. boost sensors. On the last motor the egt's stayed in acceptable ranges and boost was 55-60 psi. I live in the Denver area and pull a lot of mountain passes, Thanks for your inputs