Your mechanic did you no favors. You have a bent shift fork. If the problem was present and was then good for 1000 miles the mechanic removed the fork, bent it back to nearly
straight then put it all back together. If he had put in a new fork he would have charged you for it. If he said he could find no problem then how did the problem go away, magic? He probably didn't want to go to the trouble of finding you a new fork since the bike is 13 years old and the dealers wouldn't have the part. The problem will only get worse.
The entire engine comes apart > Head. cam chain, cylinder, flywheel electrics, clutch, oil pump, shifter, gears, shift drum and bad shift fork. This is best done by a dealer. If you try it yourself, be able to put 100 or so parts back together. Go to the site below and take a look in a parts manual. I couldn't find a free service manual for download. Yes, the link says Yamaha but you will change that when on the site.
http://www.babbittsonline.com/pages/parts/viewbybrand/1/Yamaha.aspx
To find parts, google " vintage kawasaki motorcycle parts "
Please top rate this answer. Thanks Brock!