I have a o6 Classic that I purchased used. It already had Jardine exhaust on it. IMO, with stock header, Purchase a set of Tors mufflers, triple K&N's, remove the throttle butterflies. Purchase a PCIII and TAKE IT TO A DYNO, Let me say take again, TAKE IT TO A DYNO and have it dialed in on a dyno. Most guys purchase a PCIII and snap it in, install the canned program from the factory and take off. They are only doing HALF of it. If you do not have it dialed in on a dyno you are not getting the full benefit of the PCIII. When I had mine dyno'd I only picked up 2 horses but the throttle response was so much crisper. I can snap the throttle and there is no booge or stumble. Its the type of throttle response that allows me to snap the front end up in the air with nothing more than a snap of the throttle. No clutch needed for that wheelie.
I have both, Tuneboy and PCIII. The only reason I went with a TB was because I could correct the Speedo and remove the top end speed limiter. You can not do this with a PCIII.
Or if you want to start small, Go to Ebay and purchase a GIPRO and remove the secondary butter flies. You will notice a big difference in throttle response and you get a great gear indicator to boot.
Good luck with your improvements.