I checked the Staintune website. None shown for an '03 ST4S.
You're going to have the same problem if you go with a Power Commander. You just have to know what fits. Any of the ST4 pipes will fit, regardless of year or if it's the 916 engine or the S model's 996. The difference in pipes between the ST models is inlet size. The ST2 and ST3 have 40MM inlets, the ST4 and ST4s have 45MM inlets. If you find a listing for a 2001 ST4, they will fit your 2003 ST4s. If you want a Power Commander, you need to buy the one listed for a Monster S4. The PCs for our bikes don’t connect directly to the ECU; they are placed in line between the injector connectors and the TPS connector.
On the Power Commander... First I will say that there is nothing wrong with a Power Commander. I've used and liked them on other bikes. They NEED to be custom mapped to be right. I've never had much luck with any off the shelve maps when I was using a PC. If you don’t spend the money for the dyno time, you might get a benefit from it, or you could end up with crap that you’re always messing with. For years they were the only option for us with the smaller ECUs that cannot be "chipped". The maps are flashed on the ECU and there is nothing you can adjust without software. These days, however, a Power Commander is just an extra component that can fail. You now have access to any number of aftermarket companies that offer remapped ECUs that were previously only available from Ducati for ridiculous money. There is also software available to make the needed fuel trim adjustments. For the price of the PC3 with dyno tune time, you can get a race mapped ECU that will give better reliability and better results. I say better results because of the differing “tuning” mentalities between the two. With the PC3, it is too easy to use it as a band aide to mask a problem. In other words, you tune the PC3 to make the bike run right where all you really may have needed was a proper base line tune up (TPS set, TB sync, air bleed and idle set screw adjust for proper CO and idle speed). If you just slap one on there, you may end up with a PC3 tweaked to make a poorly set up bike feel right. Fine, until you get in there again for the next valve adjustment and tune. Your PC3 may not be right any more and you will be left wondering why the bike is now running like crap. All I’m saying is if you go with the PC3 and custom tune, it is VERY important to have a base line tune that is correct and REPEATABLE. With the race ECU, it is assumed the bike’s base tune is correct and to standards just like the OEM ECU is. If you tune the basics to spec, the more performance oriented map will be right and the bike will run perfect with open air box and pipes. Simple, no extra hardware, now inexpensive and makes the bike run like it should.