I replaced my ignition box, which also acts as my cam sensor, I replaced the spark plugs, I replaced the coil. At first I thought it might have been an overheating problem as well, so I ran it without the nose cone cover, that didn't work, and today after I replace the coil, I tried to take it up the road where it died almost immediately less than a half a mile away from my house, so I can't imagine heat would be the culprit anymore because the bike wasn't 100% warmed up.
I picked up an array of different size Jets, and upon pulling mine out which was supposed to be a .072... I quickly realized that my .072 had a much larger orifice than the point .076 I was trying to replace it with. Someone had clearly drilled it out.
I had my neighbor, who has owned a motorcycle shop for years, swing up and help me tune the carb the correct way so at least I know it's no longer a fuel problem.
Just for clarification, after you fixed the carb issue, the bike runs OK until you get the failure? After the failure ( sputtering, backfiring, surging, no throttle, dies) and cool down it will start and run OK till next failure.
If this is true my guess is the problem lies in the ignition system.
From what I can read in the wiring diagram for this year bike you have an Ignition Module, a sensor plate, a coil , plug wires , plugs , an ignition switch and an ignition switch/ starter Module. Your description sounds like you replaced the IGN Module, Sensor Plate , Coil and Plugs. I would continue by checking the plug wires and the ignition switch. For 2003 models there is a new ignition switch. Check out page 12 and 13 of the Electrical pdf. The plug wires can be bad( poor continuity) and fail or arch when under stress,heat or vibration as well as the Ignition switch. I'm not familiar with the reliability of the IGN/Starter Module but hey it's a big part of system pg 10 same pdf.
Page 8 shows where the grounds are for your bike. I can't stress enough that these are clean and checked well. Countless issues are caused by poor grounds.
I found this under starter issues may help:
5. Sensor Plate and its Connecting Wire If starting still fails but the bike turns over (especially when the bike is hot), inspect the sensor plate.
Additionally, locate the sensor plate wire and follow it to the 3-pin connector (located between the frame and the left gas tank at the front of the seat). Sometimes the pin in the connection has come loose and needs to be firmly reinserted.
If they all check out OK my guess is the wiring to and from the EHC or the EHC itself is failing. Read the electrical pdf in it's entirety and maybe you will get additional ideas on what to check and how to troubleshoot.
Intermittent electrical problems can be very wacky and totally hard to find. Keep the faith and try to be very clear about what you do to get to the bottom of this issue. Any info may help one of the members come up with a troubleshooting process in addition to what I've said to help you. A check list from start to finish may be in order. Sometimes that helps to fill in the blanks and keeps things in focus. Again Good Luck going forward.