83 CR 250 Sprocket shaft

Hello Fello Left Kickers,

I am restoring a 1983 CR 250 and have rebuild the engine and put it back in the frame and hooked up the chain and the rear wheel hardly turned. Took some effort and it finally spun but thought the rear brake was on or a bearing was binding. Took the chain off and the rear wheel spun freely no problems.
Went back to the engine sprocket it was hard as hell to turn but the bike is in neutral. Can anybody help me as it is really pissing me off that i have come so far but can't get it sorted.
Took the clutch cover off and the clutch basket so the clutch was not connected to the conrod and the engine sprocket spun easily but the clutch centre shaft also spun.
If the bike is in neutral then why would the clutch centre shaft spin.
I have checked it four time putting the clutch back together and taking it apart and I am definitely positive that it is in neutral, you can feel it slip into gear through the output shaft and sprocket.

Any ideas of any kind would be appreciated as i would love to get the bike going and kick my mates ass on his old KTM this weekend.

Regards

RTB

Thanks John,
I have rebuilt the motor. Pulled it down from a wreck as the stub shaft on the ignition side was sheared off and had it stripped. When we pulled the gearbox apart we made sure all the gears and shims we stacked exactly as they came out of the bike and wired together.
It definitely feels like something is just out of alignment, making the shaft very hard to turn.
Thanks for your comments.
Motor here we come.