couple thoughts
From the info you described, the problem sounds like it is instigated by heat or vacuum. Here are the likely culprits:
Fuel: improperly venting gas tank or clogged petcock. You can rule out the vent issue if the problem resolves itself when the fuel cap is completely removed. Check this first. If that is not it, check for a clogged petcock (usually caused by a bad liner). To do this, simply fill the tank with fuel and let the bike sit for a while so the liner particles settle to the bottom of the tank. Then switch the bike to reserve and and see if the problem occurs. When the bike starts sputterig, switch back to "on" (not reserve) and see if anything changes. If the bike starts to run better, the bottom of your tank is probably crudded up with tank liner. Keep in mind that some liner particles can float, if you can visually see particles floating in there, perform the opposite sequence.
Electrical: Some 2003 bikes had a problem with the computer malfunctioning when the bike gets hot. These problems were hard for technicians to duplicate in shops because they rarely ran them enough on the road to get them hot enough to fail. If you do not have a fuel problem (See above), it is very likely this is your problem. The computers for 2003s can be hard to find out there. However, I can probably modify one of the other ones to work for you. Let me know what you find out and I will try to get you what you need. Simply shoot an e-mail to
Matt.Moore@bdm.com. Good luck. Awesome bike. Well get you fixed up.