What sort of performance/riding enjoyment improvements are you looking for? While I too own an '04 ST3, although I chose Staintune cans, I don't know that more power will really improve my enjoyment experience. I still may at some point have some port work done, maybe even some new headers and larger valves if the mood suits me.
The real performance-enjoyment upgrade on the ST3 is achieved by suspension work. Have you swapped out stiffer fork springs? The OEM springs are waaaaay soft for even the most diminutive rider. While you're in there, upgrade the fork valving. Next, lose the Sachs-Boge rear coil replacing with a Penske 3-way, preferrably with a Ti spring of appropriate rate. Use that Penske length adjustment to raise the rear end for quicker, lighter and more responsive steering. Lighter forged alloy wheels are a very nice upgrade in feel and performance, not to mention looks as well. A lightweight Metmachix alloy swingarm will also dramatically reduce unsprung mass, increase torsional stiffness in rear and make chain tension adjustments a piece o' cake. Of course the Pilot Road tires MUST go, replaced with Diablo's in my case, although some like Pilot Power's and I may give Conti Road Attacks' a go for my next set.
Creature comforts like heated grips and a GPS mount can also help but for my $$, suspension upgrades deliver the greatest improvement in riding enjoyment on any bike, including the already very nice handling ST3. Take care.