Hello Deritrend
2nd what Straight6 says.
Based on such a drastic change in clearance you have 2 choices.
1: If the Head is re-installed, take a chance, grind the butt end of the valve stem, then shim accordingly. Not advisable, just saying what others have done in the past. some with success, others not so successful.
2: The best option for success is removing the cylinder head and making sure the margins of the valves are not too thin, or that the margins on the seat faces are at the correct angles and widths. (in other words, not over-ground) which can be the case, when you see the valve stems riding too high in the head, at the tappets. If you are not sure about this, it is best to sacrifice that new head gasket and make sure.
3: Under the headline of what should have occurred when the vales were ground. With the cylinder head on the bench, the cams should have been installed, after the valve grind, and the valve clearances checked at that time. This way the person who ground those valves can catch any clearances while the head of off the bike.
On another note, It is perfectly acceptable to grind the Butt End to clearance the end of the valve stem. (Provided the valve seats and valve margins are within limits. You will need a Kawasaki Shop Manual to make that determination. It's best to grind the valve stem off of the bike and out of the head. It's the best way to get a squared cut (Grind) off the the Butt End.
If the seats, the valves, or both are too far gone, then you are looking at seat replacement, valve replacement, or both. Seats and valves are still available, but would require professional machine shop services to make sure the job is done right. (Depending on what resources are in your area)
It is ok to replace just a valve or just a seat, if one or the other was ground too thin. Just make sure they are re-ground and lapped in correctly.
If machine services prove too difficult, then you my be looking at purchasing a good Cylinder Head Core off of Ebay. This can be a hit or miss proposition, so have it inspected right after you receive it. This way if it needs to be returned you are not out of your purchase price. Focus on cracks in the combustion chamber and water jackets (Magna-fluxed) and watch out for corroded water passages, plus the notorious bevel gears. Head may need to be decked for gasket seating, but only if it needs it after a straight edge tells you otherwise.
A quality base and head gasket is a must.
Best of luck in getting this resolved, keep us posted.
Todd.