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

Your issue is failure of the clutch to disengage, nothing more. Before you start ripping everything apart you need to check out the linkage thoroughly. Are the plastic bearings in the Z-bar still there? Is the fork pushrod incorrect (too short)? Take off the inspection cover & have someone push in the clutch after any changes, you should see it disengage, a feeler gauge of say 0.025" should easily fit in between the disc & flywheel. The disc should also move by hand in neutral. If the linkage is all good then you have some sort of disc problem, it may be warped, at that point you will need to remove the clutch. It could also be an incorrect or damaged pressure plate.