when you say "new stage 2 clutch" did you get a clutch kit with a throw out bearing/pressure plate/disk? because not all throw out bearings will work with all disks. i used a new OEM bearing and act 6 puck and i couldnt shift at all, the bearing was rubbing on the middle of the disk. when i got an autozone bearing my clutch was right at the top like yours is. if you didnt get a kit you might have a similar issue.