Do you have a photo of it? Do you have shims behind the flywheel? Is the flywheel collet sticking out the back of the flywheel a little bit?

I had that problem on my buggy... or savage, can't remember which. I had to grind about 1.5mm off the back of the collet because it stuck out the back of the flywheel too far. The collet would hit the bearing on the engine and obviously stop, but it wouldn't allow me to move the flywheel closer to the engine. I think I was having the problem on my buggy. The flywheel was rubbing on my brake disks.