Have read many posts relating to this subject, seems they get muddled up with alignment bar differences, ways of measuring, it can't be done etc. etc. The key is understanding what's happening and how to go about it. It's simple shimming, but determining where and how much takes time to figure out. In order to keep this lenghty post as short as possible, I want to limit the procedure to the most common alignment problem, primary out .050 to .120 motor twisted clockwise in relation to jackshaft (secondary). Start by pulling primary, set aside but close by, remove bolt on secondary but leave secondary on jackshaft for now. Loosen front crossmember bolts, back out 1/8" or so, it doesn't really matter just so they're loose. Same with rear mount bolts. Back off torque stop(s) and and unhook torque link if so equipped. Now if you grab motor and jiggle it around, that is in essence what's available to shim around, but where to start? No beer breaks yet, the 900's sit in 4 point stance within bulkhead assembly, all 4 mounting points are important but the first one in importantance is rear mag side, because that's the one in closest proximity to jackshaft/chaincase assembly. If I'm seeking parallelism between crank and jackshaft this is great place to start, with the added ridgitity of chaincase, plus I have a bossed threaded hole on crankcase in which to run my motormount bolt into. So with everything loose try tightening the rear mag, and only the rear mag side. What happened? To see, slide the primary onto crank, just 'hand snug' and lay your alignment bar on it, now what is alignment to secondary? Better/worse? (add or remove shims on secondary to get accurate reading) If I were a betting man, I'm betting the alignment (motor twisted cw scenario) just got a whole lot better! Next tighten front pto side, any change? Check and verify with alignment tool. Try the front mag side, check and verify. That leaves rear pto side, in my experience, by far the biggest culprit in clutch mis-alignment. Now's a good time for a cold one.....By now you'll notice a large gap between inside of motor mount and boss of crankcase, measure it with feeler gauges. This where appropriate thickness shim/washer goes. But before that, just for giggles try tightening that bolt without shim and notice what happens. All that CW twist goes straight to the motor via the front rubber/urethane motor mounts! Is it a wonder these things fail so much, along with everything connected to them! Also check for parallelism on the vertical plane (Z axis), since ends of crank and jackshaft have been faced, spotdrilled and tapped, a good quality torpedo level is all that's needed, held flush on ends of shafts. Once these things are confirmed it's just reassembly, don't forget to set deflection, offset & float on secondary. I'm out!