Well I had been having this problem with my 07 gsxr600 for a while and for the life of me could not find the answer. So I talked to my mechanic and figured out that I had to get my valves adjusted (I got it done by him b/c this was wayyy over my head). He ended up replacing 10 of the 16 shims and adjusting the other 6 to spec. My bike has 8 intake and 8 exhaust valves, so 2 intake and all 8 exhaust were messed up. But
my bike has ~27,000 miles on it and has NEVER had the valves even checked.Yes stupid on my end...but I just never heard about this type of maintenance and simply kept riding.
Mechanically I'm pretty competent - I DIY all of the following on my gsxr: oil & filter change, air filter change, spark plug replacement, coolant drain, flush, and replacement.
Now to get to your bike:
I was told by my mechanic that valve adjustments need to be done routinely for all sportbikes since it's such a high performance engine (all the high revs) that the shims loose millimeters and it throws everything off.
Typical Valve Adjustment Values (quoted from my mechanic):
Ducati = Every 6k
Suzuki = Every 15k
Yamaha = Every 26k
For this reason here's how we're going to diagnose your problem. I read that you said your idle was 1k almost to 0.5k and then stall out. So normally your bike idles at about 1k? If you look up your manual's idle speed it should give you a range. For Suzuki I'm not remembering exactly but it was about 1200-1600ish rpm. I just looked up on r6-forum
http://www.r6-forum.com/forums/showthread.php?t=61170 and a guy said this:
"The idle adjustment screw is on the right hand side of the bike right under the fairing. Basically if you are sitting on the bike, (riding position) it would be right under your knee. Turn it to the right to turn up the idle. Have it idle at about 1,000 RPM. Or maybe try a little lower, and work it up little by little until it can hold steady."
1. So i'd do the same as I first tried on my Suzuki and see if turning the idle a quarter turn clockwise to raise the idle and see if it solves your problem.
2. I forgot to ask you if your bike stalls worse when it starts, cold start (or will it idle on its own?).
3. You should ask yourself with 8700 miles on it when's the last time you did a tune up on it? When was the air filter replaced and ur overdue for your spark plug replacement if you havent ever done it. If your bike can't breathe, then it'll stall also. Is your gas mpg being affected? This is usually a good indication of a bad air filter and/or spark plugs.
4. If all of this fails I'd check to see if your 2003 R6 has secondary butterfly valves by the throttle body and see if they open wide with the air filter pulled off on a cold start.
5. If the secondary throttle bodies move then find out on some forums how to check to see if your TPS is working correctly. You might try throwing the bike in dealer mode (look this up on forums, usually a paperclip connection under the seat) to see if it throws a code letting you know your TPS is bad.
6. If all this fails I'd then start thinking about your valves and getting them adjusted, shims replaced.
Just remember in the end it's totally worth it! You learn so much from researching all this that you end up getting to know your bike really well. A lot of guys on this forum have got tools for you to use if you dont have a garage or tools. Just thought I'd chime in since I know I was frustrated with the problem.
Good luck dude!