"darealblaster" is right, you need to do a plug chop.
to do it ride your atv at full throttle, and without burping the throttle again or revving the engine after,(or wrecking your blaster) immediately kill the engine and safely coast to a stop.
remove the spark plug dark brown or black and it's too rich, gray or white and it's too lean.
also do an idle plug chop, since the pilot jet controls idle you'll want to see what the plug is saying on both idle and full throttle
so crank it up, let it run for a few minutes without touching the throttle at all. just let it run at it's idle speed, even if that's idling high. then kill the engine and check the spark plug electrodes' color.
if it's tan on the full throttle then you know you have the right main jet, but gray or white on the idle plug chop then you know it is too lean on the pilot.
what you are looking for is a nice creamy tan color.
it does sound like the pilot jet is a little small. (the smaller jet)
when you did the big bore kit and the carburetor did you rejet it?
and did you disconnect the over-rev swtiches and module?
if yours is 2003 and up the over-rev module will be in the cdi and can't just simply be unplugged, but the guys here can tell what you'll need to do,
on earlier models the over-rev module is seperate and is located under the hood, with a triangle shaped connector.
what brand big bore kit did you go with? and did you have it ported?
if you went with the vito's it came with a jet kit.
you'd most likely need to use the largest main jet (340) and the stock pilot jet.
the pilot jet included in the vito's kit works with the stock carburetor, and is a .30
but the stock pilot jet is 32.5
which is most likely what you would need for that big 34mm carburetor on idle.
however if you have a keihin carburetor the numbers will be different as the jet kit included is for the stock mikuni carb.
I think the mikuni jets will screw into the keihin but don't force them if they do in easily. you'll have to buy a different jet kit for yours.
I don't have a cross over for the keihin numbers. sorry