Welcome Hairymatt, first thing I have to say, is to stop right where you are, if you have the flywheel removed .
With the flywheel removed, the crankshaft can move forward slightly and dislodge a thrust washer that is on two pins at the back of the engine case .
You need to remove the front cover, place a short portion of a 6mm allen wrench in the bolt head that holds the alternator on, then put the front cover back on so it prevents the crankshaft from moving .
If this easily deform washer gets off of it's pins, when you put the flywheel back on, the crank shaft will be locked up !!