I recently inherited a 1999 kawasaki bayou 220 for my 12 year old daughter from a well meaning co-worker.  It was parked last year with clutch troubles. He tore the clutch side engine case off, as well as the primary clutch and secondary clutch and shifting mechanism. It turns out the secondary clutch disks are bad. My question is, how can i be sure the transmission in in neutral when re-assembling the motor? The clymer manual just says make sure transmission is in neutral. How do you check? Thanks!  

move the shift lever to "N" jack the rear of the atv up and turn the rear wheels see if the stop.
if so it is in gear.
move the shift lever until wheels spin freely.

if the chain is off of the atv turn the clutch basket and see if the front sprocket turns with it.
if it turns then it is in gear.