Had a long off season... Became a grandfather, went on a backcountry elk hunt and took a temporary promotion a work. After all that... I finally got the time to replace my stator and rotor. Put everything back together. New oil. Fresh charge. Fired the bike up and after about 5 minutes.... Dead again. Battery down to around 11.50 volts. At this point I'm guessing bad battery or bad regulator. What do you guys think?

 

I'm thinking that it's running on the power that's stored in the charged battery until it's exhausted and once it's gone..........it's gonna die. So I believe it's the regulator that's the problem. The regulator isn't putting out enough juice to run the bike and charge the battery at the same time.

 

Surely then though the battery wouldn't have enough juice to start the bike again, and the OP says it's starts up fine after cutting out. My FB wouldn't start if the battery was even slightly weak, it would spin up fine, but not start.

Check the tank is venting properly. If this problem started straight after filling up, it has to be related to that. Check filler cap and tank vents etc When the bike next cuts out, open the fuel filler and listen carefully for a rush of air into the tank.

 

I'll check the tank while I'm at it but I'm inclined to tHink it's the regulator since the battery will charge then drain when the bike is running

 

Ok another update. I charged the battery then started the bike while monitoring the voltage on the battery. It runs great for a while (about 3 to 5 minutes), the voltage even goes up to 14 while it's running. Then the bike just dies as if I had shut it off, accompanied by a back fire and a small flame popping out the pipes. When it dies, the voltage drops quickly down to below 12, but not before it dies.

 

3 to 5 minutes run time at tick over is not enough to replenish the battery from the drain it takes starting the engine. Thats why after it cuts out you see a voltage drop.

Have you tried running with the filler cap lose? I bet it runs and runs.

 

I'll give that a shot tonight

 

Loosened the gas cap so there was plenty of air flow. Started up, ran for 4 1/2 minutes then dead like before

 

Damn, I really thought that was it.

The flame from the exhaust when it dies would suggest that the exhaust is filling with unburnt fuel then igniting with the last spark before it dies. Similar to a trick my reprobate friends use to do before fuel injection of hitting the kill switch for a few seconds at say 60 mph then flipping it back on. The pipes would be full of fuel and would result in a massive backfire.
So maybe this is electrical after all. I've had problems myself with old components developing high resistance whilst hot.
If the voltage is good whilst running that would rule out the alternator, so it has to be something between that and the plugs.
I can't help thinking that it has to be linked to the time you filed up with fuel though, as it started straight after that.

 

May want to test your crank position sensor. There's an ohms test in the service manual or electrical service manual. Can't help you with the #'s on that test right now, books are all packed & my memory sucks.
I know & understand you don't want to randomly throw parts at it, but buying a CPS wouldn't be a loss if you didn't need it. I ride with an extra 1 just because it's failure can be a show stopper. You could leave the old one in the harness, install the new one outside the harness (avoid the pipes) just to see if it works.
Just another suggestion.