Rotational Clunk noise with engine disengaged

Thought I would throw out this problem and see what I get for responses.  I got my 82 KZ100 last fall.  It needed a carb clean and general tune-up - it sat for a season.  I rode it briefly before putting it away - only issues I had fuel leaking out of my carbs once I parked it.  This spring I sent it out to a local shop, they went through the carbs and told me that the bike jumps out of second gear, especially under light load.  I picked the bike up as is and have been riding it a bit.  I've put approx 400 miles on it.  I felt the second gear issue and have been shifting first to third to see if I like the bike - before I dump more cash.  Regardless, I enjoy it a lot.  This is my first street bike (I rode dirt and grew up with musclecars). 
   I am an Auto guy, so I haven't wrenched on bikes much, but have worked in the Auto Industry for years.  The shop also fixed a shift shaft leak (although it still leaks) and tried flipping around the shift shaft because it was worn.  I feel like the clutch is disengaging full when I have the clutch lever pulled in and they even said that test riding it they got on it to make sure the carbs were jetted correctly, etc. (I had them put on a Delkavic 4 into 1 system).  Now I am getting a rotational noise even with the clutch lever pulled in-  and have noticed that the chain has way to much slack. approx 2.5-3 inches on the center stand.  I found a thread and this could def be the new noise and vibration I feel in the left foot peg.  I just wanted to see if there were other things I should do given circumstances.  I wonder if a shift got missed and they bent a shift fork? or adjusted the clutch and now  a worn 2nd gear dog is popping out worse than I initially rode it?  Any ideas would be appreciated.  I just picked up a complete 2nd motor that I can possibly scavenge parts from.
   I appreciate any help!  The KZ is going to be a permanent part of my garage next to my '67 G.T.O!
  Thanks,
       Dave

Howdy.  I would do the basic clutch & drive chain adjustments as per the FSM.  Normal slack is ~30-35mm measured at the tightest spot in the chain.  Since yours is an 82 model, be sure to reference the 82 supplement (pg 10-18) for doing the clutch adjustment:  it's backwards from the procedure listed for the 81 model.  Also, you might want to take a look at the front sprocket to make sure nothing is amiss. 

Kawasaki service manual.  There's an 81-83 pdf available that should cover your motorcycle.

ps: is the motorcycle an Ltd?

Yes, its an LTD, That sound like the best starting point.  Thank you.
                                -Dave
 

A few years back I had a rythmic regular  clunk noticeable at about 50kph (30mph) and which I could feel at the left foot peg. I figured it was the chain but with bike on centre stand the chain slack was perfect. Then I realised that I had put newer rear shocks on the bike which were a bit longer than stock and sure enpugh when I examined slack with bike off the stand and both wheels on the ground there was a tight spot.

I also removed the transmission cover which is behind the front sprocket and had a good poke about to make sure everything was ok. I was worried the bearing might have been rubbished