Engine stutters with clutch engaged

I was coming home from a great ride yesterday and less the a mile from the house the engine just started sputtering out of nowhere. The gagues also dropped like the engine was shut off but it was still running. When I pull in on the clutch, it stopped sputtering though and ran perfect. But as soon as the clutch is engaged, it sputters again. The only other thing is while cruising along yesterday also as I passed a truck I heard what sounded like a huge backfire, but I was passing an old beat up truck at the same time so I not 100% sure if it was me of him...I"m thinking me though. I've only had the bike for about 300 miles and this is my first CBR...any ideas??

one thing that would help is knowing what CBR it is, and what has been done to it.

It's a 2000 CBR600 F4. I haven't doen anything to the bike but as far as I know the only mods are fender eliminator, low profile turn signals, Yosh exhaust, and zero gravity windscreen. I'm pretty sure it has not been jetted or has aftermarket intake.

i guess the first things to check would be all the obvious ones.
 
Definately got gas (dont trust the low fuel light), when idling will hit ever 8000 rpms, check the air filter to make sure its in good shape, check the oil, check the coolant.
 
Might also want to see what happens if you put in on a rear stand (rear wheel in the air), and engage the gears to see if it still sputters. Kind of a no load test.

Alright thanks a lot. I'll try all of that tonight. I don't have a set of spools yet though so I can't test that one but I'll be sure and check out the air filters, oil, and coolant tonight. Do you think it might be something with the fuel filter too? It does have plenty of gas in the tank too..

i fresh fuel filter never hurt. Seems to be forgotten a lot on most bikes. When I got my bike it had like 30,000 miles on the factory fuel filter...needed replaced bad

Hey guys..just wanted to say thanks Scufdog for the help. I finally got around to working on the bike some more and it turned out to be the spark plugs!!

So anyone who has an undiagnosiable problem as to why the engine runs rough while in gear but not in neutral (even when reving up) it could be the plugs even if you take them all out and they all look good. Looks can be decieving!! Change em anyway!!

cool, glad its running again.