okay, this is no help to you now, and you have figured it out by now but, always empty your tank for long term storage (more than 6 months). Gas will turn into a sticky, gooey shelac with age. If you are just gonna store for winter, put some fuel stabilizer in it to preclude the breakdown.

If long term storage, I drain the tank and then run the bike until it stops to ensure all of the fuel is out. For winter or short storage (3 months), I put Stabil in with the gas. I always fill the tank and then add the appropriate amount. You can run the bike with the stabil so it doesn't hurt anything. Put in the recommended amount! Don't over/under add so it can do it's job properly.

Again, not trying to be a smart ass, but this type of maintenance will preclude the issue you are dealing with now. Bad/old fuel can really gum up the injectors if not treated properly. Sounds like your issue is just bad fuel and not contamination to the system.