If you know you are going to modify a bike extensively then you must go with the 2.3 because it can be done at this time. The 2.5 feels like it does not need much and a Penner tune will wake it up.
Before you modify an engine you need to be clear about what kind of power profile you are looking for. The older Gurus recommended a torque build for me since i live in the mountains and it has been the best choice for me. The higher HP carpenter bikes need to rev quite a bit higher rpms to get that max number you are lusting for. I rode one bike that needed to get over 4500 rpm to really feel like it was awake. At 7000+ things got real. The bike I own get good power from 2200 and up to a max rpm of 7250 with no drop off at the rev limiter.
I need a qualified Rocket captain to come over to my house so we can race my two bikes side by side a few times and see how they fare. Anybody wanna come over?