HELP!: Gearbox "clicking"; bike will not roll in neutral

If you paid someone to split the cases, then your first move should be to take the bike back and demo the problem and ask them to make it right. If it was the previous owner then, based on your description, it would lead one to conclude that he did made some reassembly mistake. There’s an outside chance it could be a broken KIPS advance shaft. While it’s not unheard of for a broken advancer shaft pin to migrate into the transmission, that does not seem likely in your case, because with all the clutch work you’ve done, you would have noticed that broken part and/or the evidence of damage to the basket. It’s been my experience with the clutch that you generally don’t need to mess with the engagement shim. However, make absolutely sure that you have the two spacing washers in the correct position (see link). If either one is not there or in the wrong location that will screw up the engagement. That messed me up the first time I took my clutch apart.

http://ourworld.compuserve.com/homepages/rushbe/clutch01.jpg