Sorry If this question sounds ridiculous, but I've looked everywhere and can't seem to find the answer. My question is what causes the torque on the rev up vq35de (05-06 350z) to be lower than the regular vq35de(03-04 z)? Any help will be appreciated. Thanks guys in advance.

higher compression, different intake design, and a slightly different variable valve timing system. and some ECU tuning also.
and direct injection too.