CycleTech

Check the carb vents also.

Im assuming you have the clutch basket off so you can spin the tranny??

Sounds like you have a problem with the shift drum and or a bad fork. Are you spinning the countershaft while trying to shift? You should get the rear off the ground and spin the rear wheels while trying to shift through the gears so that the gear dogs can fall into place while you are spinning the drum through the gears. If it wont alow you to do so then you will need to get into the tranny and report back with your findings or pictures.

If both carbs are running lean then check for a fuel starvation problem. Fuel tank vent?

Put a time-sert in it. If you don't know what that is then look it up. Its the best thread repair design Ive ever used and I use them all the time(Powersports Tech).

So what happened?????

That jet you found is the main air jet. Its located on the airbox side of the carb throat and its for air to the Emulsion tube/needle jet. It would have no effect on starting and how the hell did it get in the bowl?!?!? Stock to 2001 spec's call for a 1.6 M.A.J (Main Air Jet). Make Sure your carbs are synced and the idle adjustment is low enough that you are building a good vacuum to pull the fuel through the choke circuit on startup.