Have a 04 250ex that I just did an overhaul rebuild on so had to split the cases an what not. Believe to of installed everything correctly motor wise, have a bit of trouble with clanking coming from inside the clutch area of the case and the output shaft that connects to the rear wheels from the motor. Reason I say that is because when I’m in every gear except for second I believe, I get a very bad loud clunking noise an I can hear it from both areas, kinda like something’s binding up. So if I start in second everything’s fine runs perfect an revs out an when I go to upshift or downshift it’ll still works an the machine will recognize I’m in different gears as I’m able to accelerate without hitting rev limit. It’ll start to clank and just is a very bad sound overall even tho it’s still functioning right through the gears. Also cannot find neutral at all. So I’m having to ground out the neutral wire to the motor to be able to start it. Not sure if I messed up something within the tranny any advice would be greatly appreciated. Can link video of what’s going on here in a bit currently at work

 

You have something seriously wrong if you can't find neutral, never mind the clanking. Take the clutch case back off and inspect the selector mechanism, look at the clutch operating lever too, as this can get bent and rub against the clutch, not much else could be making a grinding noise except the gear selector forks in the centre cases, which would demand another complete strip to fix.