It might sound kinda random, but I discovered a neat little trick for perfectly aligning the clutch disc. I was too cheap to buy a metal clutch disc alignment tool and just reused the old plastic one I had laying around. Sure enough, the disc wasn't aligned properly and the input shaft of the tranmission refused to line up with the pilot bearing. I sure as hell didn't want to lower the transmission down again and rip everything apart (I was working all alone at 2AM) so instead I bolted the slave cylinder back to the bellhousing and pressed the clutch in. The input shaft was already through the disc and pushing forward on the bearing. Pressing the clutch disengaged the clutch just enough to allow the input shaft to line up with the pilot bearing. The genius of this pull-style clutch is that the actuation on the slave cylinder actually pulls the transmission forward into place. Of course, you have to make sure the slave cylinder engages the clutch fork before pressing the pedal in. Otherwise the the slave cylinder will probably spit its guts right out.