My r6 was last rode in July, I kept gas it in and I stored it inside my house. I started it every once in a blue moon. The last time I started it was a few months ago when I drained the gas. Saturday I put some new gas in and tried to start it. It started ok...cranked slow, but would not idle. Once I let off it would die. It was 36 degrees out so I took it for a short 5 mile spin, while riding it ran and idled fine at stops. Once I got home, shut it off and started it back up (was still at 170ish degrees) it wouldn't idle again. The bike has no cat, a pc5, and a just a gytr slip on. It was dyno tuned at a highly recommended yamaha dealership.
Would the battery being a little low cause this? (my charger is at work at the moment) or could it have to deal with the cold weather and the bike was tuned in the 80's?

 

-in this age of sophisticated electronics...just have the shop re-load your map. they should have it on file. I don't like power-commanders or piggy-back emulators, just my opinion. I have nemesis software on the ducati and a "tuneboy alternative" on the Triumph...both use factory ECU but change parameters internally.

 

Have you pulled codes yet?

 

this sounds like your culprit, but whatever it is it has something to do with your pc. im assuming your bike starts without any problems now so your stator did its job as far the battery is concerned so thats not the issue. ride it to the dealership since they are the ones that mapped the pc and have them look at it.

 

With FI, draining the fuel does not help for long term storage. Fuel tanks are much better sealed these days, 4-6 months fuel with stabilizer should do fine to stay in the tank.
Empty out the fuel from the tank deos not empty out the lines leading to the injectors, IMO the injectors are glogged up.
I would try mixing fresh fuel with SeaFoam and just run the bike through the rpm range for a full tank, that should clear out the injector flow to acheve smoother idle.