You shouldn't have to unless when you slide out the bolt it's hitting the exhaust. Both 650's I owned had aftermarket exhausts with lots of clearance. It the bolt is hitting the muffler when sliding it out you may need to just slide the muffler off from your the engine and not from the head.
Also...it's been so long since i've seen a KZ650... The aft portion of the swingarm where the axle slides back and forth for chain tension should have bolt going down through it. Remove this bolt and remove the small block inside the fork and you should be able to pull back the wheel for removel...
Let us know what you find out.
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