Thank you guys for trying to help me but i found where it goes. Even though it looks like some kind of pump part, its actually just a bushing.
For anyone that stumbles upon this thread its a bushing that goes into the end of the transmission main shaft and the KTM part number for it is 78033001110.
I just did mine a couple months ago, looks like you got the wrong airbox to me. When i did mine, i reuse the stock (2000) airbox and cut up my old black rear fenders to fill the gap, looks really good.