Thanks all for the replies.
So I did a leakdown test. Couldn't hear anything escaping.
Went ahead and replaced two more shims to bring them into spec. Just turned the bike over and the ticking is worse.
I think I may have figured out part of it though. Whenever I inspect the clearance on the suspect valve I get different measurements depending on where the lobe is pointed.
If I point the lobe how the manual says, away from the bucket, I get too tight of a clearance which points to replacing the shim. IF though I take the measurement with the lob pointing just off in either direction I get the correct clearance.
When it cools I plan to tear it down again (I am getting VERY good at this valve shim job....) and checking my theory as well as the cam lobe itself.
Would there be any good hints? Discoloration or anything like that?
Also, any tips for diagnosing an exhaust tick? I think it's contributing to the noise slightly.
Kawasaki changed their cam positioning methodology over the years. I prefer the method they adopted for the later year 1000/1100 engines, which incidentally happens to match the Suzuki GS method, which employs a very similar engine configuration. With this method you position the cams such that valves are adjusted in adjacent pairs where both are on their base circle. This method is simple and foolproof, and assures the adjacent valve isn't depressed and pushing up on the cam, skewing it in the journal clearance.
The method as detailed in manuals like Clymers is just flat out wrong.