I just put the starter clutch in on my bike. I have a clymers manual as well. Make sure to remove the spark plugs, it will make turning the engine over MUCH easier if you haven't already done so. Make sure to mark the edge of the tooth on either side of the timing mark so you can locate the mark as you install the flywheel. Also if you haven't already make sure you have removed the rear cam sprocket cover from the cylinder head. Now throw the flywheel nut on the crankshaft and bar over the engine a few times until the woodruff key on the crankshaft aligns with the dot on the cam chain drive assembly. (the gear just up and to the right of the crankshaft) While doing this, the rear cam sprocket also has a single dot on it(it's timing mark. It lines up with a sharp pointer on the rear cylinder head. You will have to bar it over a few times for them to align. Once they are both aligned your good to put on your starter clutch. Make sure you have found the T mark on the flywheel and marked it with something like a paint marker. After you have it on put the alternator cover back on and see if the flywheel aligns through the cut out in the alternator cover. Let me know if your still having issues.