I'm assuming you converted to non-modular? If so, then the kit should, most of the time they do. Double-check packaging and see. If it isn't there, then you might need to make a phone call or just order that one above. My clutch kit didn't come with an alignment tool either, but it wasn't needed since I'm still modular using a kit with the factory flexplate. Not sure exactly, but in a modular setup does an aftermarket flywheel replace the factory flexplate or is it a part of the kit?
-Ben Black 1999 RS
Basic mods and a South Bend OFE-SS Clutch ~150bhp.....for now!