Do this tomorrow - sit by the side of the bike on the gear shift side, with your left hand operate the gear shifter, and with your right, rock the rear wheel back and forwards (engine off, keys nowhere near ignition). You should be able to shift through the gears, by hand. If you can do this, then maybe it is a clutch problem (such as the clutch not fully disengaging when the engine is running, which means the gears will be difficult to change), if you struggle with this and they get stuck, then it is not a clutch problem, and more likely the gear shift mech / gearbox.
I would read the service manual I linked to in my post - especially around the clutch adjustment and free play. Your owners manual may also advise you on how to check and adjust this. There is normally an adjustment at the clutch itself (on the push rod assembly), and one or two adjustments on the clutch cable, follow the manual. Preferably (if you have the casing still off), check that your clutch lever is actuating the pressure plate properly after adjustment, but this isn't absolutely necessary.