a couple questions

hi could someone tell me what the difference is between a cat 3406e set at 475 hp and one set at 550 hp some guys tell me its just the computer setting. and others say the 550 has bigger injectors, bigger turbo and a bigger radiator.
my other question is once in a wile my truck acts like it is missing. it does it when u got ur foot on the pedal. leave off it goes away get back on it it acts like its missing again it only does it once in a wile and only for a minite or two then it goes away and runs fine i checked the codes how u turn the key on and hold the cruse and the check engine light flashes 5 times pauses and another 5 times. thanks for ur help.