I could bet you that your problem is the sidestand switch has gone wrong!
Or, when you dissasembled the clutch you forgot to re-adjust the "butterfly" nut that regulates the clutch!
Plus, set the clutch lever on-the-fly adjuster to around middle position and leave some very small gap on that "butterfly" clutch nut because when you reassemble the engine case and fill it up with oil, it will "tighten" the clutch a bit!
This could be your problem!
It took me a couple of tries to make it work perfect on my XT600E!