The tuning from 7 to 9 doesnt surprise me at all. Visit with Andy about that. A cam will make a difference there. Is your head ported at all? Are you running springs other than stock? Have you tried taking the gear lash out of the CP3? Stock CPS? Converter stall is stock?
There will also be many other variables to compare HP such as worn driveline parts, synthetic fluids or not, auto versus manual, tire size (which was probably one of your best gains in recent monthes), gear ratios, miles and wear on engine, etc etc.
Im rebuilding a couple 04.5 and up CR's next week with larger displacement, better cams, and a few other things if your interested in coming down and watching/ helping. Ill be also cutting rings and installing larger springs in them as well.
Also if your interested in doing a payment plan Id trade your engine minus your mods for one of my fresh larger displacement engines for ballpark of 1500 exchanged. Im just throwing one in a mega cab for resale so it makes me no real difference.