Exactly, if you got a CEL, you might be able to still read the code (the ECU stores it I think) even if it is not lit anymore. That would be a good start. If you have gas in the tank, you are probably ok, I just ran mine to low and I think there was some water in the fuel. Unless you are really low on gas like I was, I don't think that is the problem. I'm not sure how you intend to drain the fuel, but I would not recommend doing that unless you know you have to.
You could also try a jug of HEET fuel treatment, that should get rid of any water in the tank. A can of Sea Foam in the gas tank also can't hurt.
But anyway, get the code read, and bring the number back to the forum and we can tell you what it means.
Good luck,
Bart