Motorcycle Repair: KZ650C Clunking at Idle, car spark plugs, random intervals

Question
Greetings, I apologize for the long post but I didn't want to miss anything that might be helpful to you.  I have a KZ650C which recently had a tune up service at http://shinysideupmotorcycleservice.com  This was the first service it has had since I purchased it about 6 months ago.  At the time of service, I was told that it had been fiddled with quite a bit over the years.  Had an aftermarket electronic ignition which was supposedly notorious for failure, had generic car spark plugs in it, an aftermarket 4 into 1 exhaust and parts of the carbs had been bent to try to rectify certain problems that were out of the scope of adjustment.  Big clouds of rich black smoke would billow out on startup and it was getting about 15 mpg/hesitating significantly under load then surging forward.  After service, it is certainly much more responsive but I'm still seeing some items that are concerning.  

Upon getting it back, after coming to a stop, it would idle fine for a moment, then the tachs would drop slowly as it made an ocasionall clunking sound until the engine stalled.  Putting a higher heat range plug solved the stalling problem but it currently still makes a sporadic clunking sound that can be felt through the frame.  It's almost the same type of sound that the bike makes when shifting to first at a stop but lighter and not so pronounced with an almost unnoticable "grinding" quality.  This only happens at idle and generally doesn't happen when I've just gotten off the freeway, largely occuring only in town and happening at seemingly random intervals every few seconds.  Throttling up to around 1300rpm's from the 1100 that I have it idling at seems to stop the clunking noise.  At about the same interval during low rpm riding (less than 2000rpm), I notice a slight roughness or sporadic surging but given sufficient throttle, the problem goes away entirely.

Answer
Hi anthony,
           The clunking you hear might be coming from the cam chain...When was it replaced last?I would make sure the carbs are in sync....and check the cam chain...sounds to me as if the carbs are out of wack...15mpg should be atleast 25 at min and that is harping on it all the time.P.s. tun the idle up too 15oo and see what it does....glad i could help.......dan