Yes, IF it isn't the clutch giving a Problem, You should be able to start the bike in gear with the clutch fully pulled..
Some times the DRAG against the clutch pates will make it hard at first to start the bike.. Breaking them loose by moving the bike MAY help.
(clutch handle pulled).
Lots of maybe's but first off IF the tranny is stuck in Two gears, it may be a shifting fork problem.
Can the bike Move when the clutch is pulled IF SO it should start with the starter when the clutch is loose.
signed....BUBBIE
Another thought ,IT could be a compensator or a bad chain calked ???? Lots to look at. IF all the above fails to help,,,,I would start on the removal of the outer Primary cover. & LOOK WHY it won't turn over with clutch pulled...