The alignment tool isn't perfect. If you just let the clutch hang on it, it will end up drooping slightly. I had to hold the clutch up with one hand, continually re-centering it on the alignment tool, while I slowly tightened it to the flywheel. Once you have it mostly tight, remove the alignment tool and take a good hard look at how well it's aligned with the flywheel. Re-seat the alignment tool a number of times. If it isn't perfectly smooth going in, then your tranny won't go in either.