Need help with rough running bike

[rm3studios]

Sorry for this being long winded but want to cover all my bases to make things easier, and bounce my thoughts off you guys.
Got my 01 last year, and it ran great. Put fuel stabilizer in, and stored it for the winter. I went to start it and it wouldn't stay running. Got it to run long enough to take it for a ride, and it was a rough one. It was really struggling to get going. It would come out of it for a bit, then run rough again (then eventually stalled). Took the plugs out and one was fouled and another didn't look too good. They looked like they hadn't been changed in a long time. Changed the plugs, fuel filter and air filter while I had everything off. In the air box I had about 4 cups of gas . I think it was from the cylinder that wasn't firing. I'm waiting for the new air filter to come in, but runs much better. Still rough though if I get on the throttle. There was a mist of gas going into the air box, but I think it is from the fuel filter. I got the wrong size (1/4 instead of 5/16) and gas was flowing by the vacuum hose and somehow sucking it into the air box. I think the leak of gas was starving the carbs too making it run rough, because if I really tightened the hose clamp I could get a higher RPM before it would start getting rough again (but not enough to stop the gas leak). The mist of gas in the air box stopped too. Gas was still leaking out around the fuel filter, but not all over the air box hose anymore.
If after getting the correct size fuel filter and new air filter it's still acting up, what should I look at next? Carbs? Also I think the drain hose for the air box is clogged. How should that be cleaned out?

[Kreylyn]

I would pull, clean, test, and verify the carbs are working right and not allowing fuel to leak past.

I would check the petcock cause it sounds like the "vacuum" issue might be associated with that from what I understood of your description.

I would use fresh new gas... flush out the old with new, clean the tank, so on.

Krey

[rm3studios]

Thanks Krey. It was hard to explain, and I probably made it harder haha. The fuel line runs past the hose that goes in near the top of the air box, and is touching it. I think when the gas was leaking out past the fuel filter and onto that air box hose, it was getting sucked in. I was looking into the air box while it was running, and I didn't see any fuel coming out of the carbs anymore (it definitely was before I changed the plugs). I'll dump that gas and check the petcock too.
To clean out the drain line on the air box, should I blow air through it, or is there a better way?
Thanks again Krey. I feel I will be up and running soon

[shpielers]

+1 on dumping the old fuel. I doubt it'll make everything 100% better but it's the easiest thing to do and likely making existing issues worse.

[edromero]

Thanks Krey. It was hard to explain, and I probably made it harder haha. The fuel line runs past the hose that goes in near the top of the air box, and is touching it. I think when the gas was leaking out past the fuel filter and onto that air box hose, it was getting sucked in. I was looking into the air box while it was running, and I didn't see any fuel coming out of the carbs anymore (it definitely was before I changed the plugs). I'll dump that gas and check the petcock too.
To clean out the drain line on the air box, should I blow air through it, or is there a better way?
Thanks again Krey. I feel I will be up and running soon

All you have to do to clear out that air box drain hose is to remove the plug from the bottom of it and let it drain. Then make sure to plug it back up. The drainage tip is located on the right side of the bike, right about under your foot peg (midpoint of the bike). You will see 2 hoses protruding, pointing toward the road. One will be capped. Make sure to recap it when done