Clutch issues. Can't put gear in while engine running

Slick;You're not getting it are you? Re-read posts 1 and 4.
The TO bearing made contact. The OP says so, and the bearing shows it. Yeah a part of the spring is sticking out,and the TOb hit that,and it also hit the other coils. But the TOb should never have gone that far, in the first place.
Unless the disc is way too thick and the PP was not reset for it's thickness; this is totally a ratio issue.
If the disk was too thick, the OP would have had trouble fitting the linkrod between the Z-bar and the fork. He doesn't mention that.