With aftermarket Cans on... your bike is more than likely running too lean the engine temps will be higher than normal and the idle will be up and down as the ecu tries to trim out the fuel end ignition to keep the thing running.
Also you can burn out the ignition coils as they can only take so much heat for only so long before they start to die which leads to more idle speed problems and kills the battery if all this goes on long enough you may even burn the valves.

best thing to do i think is get a (proper fuel map / power commander)
a new battery.

 

I'd like to get an adjustable PC3, recommend a specific brand?

 

Leaving the lights on with the fans running and leaving it on for 10 minutes will drain the battery quite a lot, that's why it wouldn't try for long.
Charge the battery and i bet it will start again.
Doesn't mean that will cure starting problems when warm if it does it all the time though :fact
Do you have the CAT removed or just slip ons ?

 

Yeah I let it sit for a few minutes and it started right up.. the CAT is still in.. just slip ons.. previous owner did it, it backfires like crazy too.. switching gears and constantly at low RPMs.. I'm thinking he did a piss poor job at installing them because he did a lazy job with the HIDs and tail light.. blinkers or brake light doesn't even work.. plan on getting a custm relay and some flushies soon though.. maybe that will help.

 

So I try to start it and it doesn't turn over at all. I hear the fuel pump, lights come on as usual, tach bounces to max and back.. but when I hit the fire button, nothing.. it sounds like it's trying to turn over but the cranking gets slower and slower until I get nothing but clicks.

I left it alone and removed the seat to get the battery out and tender it, but just before I removed the battery I tried to start it and it started right up.. the idle is kinda up and down but it seemed ok.. turned it off and tried again and it started again.. so.. would this indeed just be the battery or something more serious?

Acts dead, then fires right up later... From that it almost sounds like you may have a loose terminal. Charge up the battery, make sure your connections are tight, and don't leave the key on any more than necessary when it's not running. :fact

 

Yeah.. lesson learned.. I've done it before with other bikes.. to test lights and such.. never had an issue, maybe it's just the R1? Figured I'd let the fan cool it down but never thought it would kill it like that. Ah well.. I know now. Glad I was home and not at some random gas station out riding..

 

Resolution?

I am having a similar problem, except I had the bike on for about 2-3 minutes after riding for about 15, tried to start it to move down the street a few spaces, instrument gauge lights up, fuel pump primed, no start, just turned over a couple of times like its trying to start. I push started it and was able to ride home with no issues.

Was it your battery? I'm having mine tested tomorrow, its over 2years old.

I hope its nothing else....

 

Last time i rode mine was 2 weeks ago , and im still trying to figure out wtf is going on ... i got caught on rain , made home safe , but since then my bike wont start ..
Have spend 150 bucks on new stater relay and new battery and all i got is a click from relay ... it pop start and runs perfect normal ... comom is 09 with 6k miles ... YAMAHA NEVER AGAIN !!! i hope is not the stater cuz it cost 385 plus taxes and it is a pain in but to get there ...