I had lots of fun with my 06 GT and it actually ran really well for what it was. I do agree that the s197s are a much more comfortable car compared to the sn96s and the 3v does respond well to mods (plus the cam choices sound awesome).
Lets start with the easy items and pull some plugs out and see what we are looking like as far as detoniation goes. Then check the obvious fluids such as oil/coolant to see if anything seems out of place.
No CEL?
Car has a nice stance to it and I bet it feels great with the MM parts. It's amazing how much suspension will improve a ride and the general feel of the car.
What type of numbers are you looking to achieve?