I am a little late coming to the party on this one and correct me if I am wrong, but there appears to be some question on what was actually done to your bike. That being true you really need to take a good look at the engine and see if things were replaced that you can SEE. Check gasket lines and sealing surfaces, do the gaskets look like they have been replaced? It should be relatively easy to see if new gaskets have been installed. I am not sure how many total miles you have on the engine since the alleged rebuild but you should be able to bring the pistons up to top dead center one at a time and look the the spark plug hole with a small flashlight and examine the top of the piston. Does it look new? Is it relatively carbon free? Certainly you can buy a small scope to peer into the cylinders and that would be a really good option so you could see the cylinder walls, but knowing the pistons looked fresh would be a real bonus. If you know anyone in the automotive repair business many of them have these scopes and may be willing to come over to where the bike is to do an examination for a small fee, or perhaps you can take the bike to them It isn't difficult at all, spark plugs out....scope lens in. I would be surprised if your mechanic installed pistons and didn't hone, or bore the cylinders. If the right type of scope is used you should be able to at least see part of the valves, but may be not all of them, but once again it would give you an idea if any valve work was done. So far almost no real mechanical knowledge or work has been needed but you should know if your mechanic is being truthful about what was done.
To follow up on what has already been said, after doing a visual examination you can get to a really good compression test. I like to do at least 2 of them to verify my results. Each cylinder must be done the same and make sure your battery is up to snuff for this. Many times guys forget to hold the throttle completely open for each cylinder and they get false results. Five or six revolutions of each cylinder should be enough for max compression readings but you many need a few more. By this point you will have a lot more knowledge about the condition of the engine and what was done to it. You could report your findings back to us here on the forum and we could offer guidance on what do to next. You just have to accept the fact you want to learn how to do this stuff or at least the basics so you can make an educated decision on what to do next. There are things even the best of us can't do, or won't do on our own engines. I won't mess with a valve job or cylinder boring. Both an an art that requires repetition to get good at, plus the milling machine I have isn't big enough to handle boring a cylinder block. So I am relegated to taking those parts into what I have determined to be a high quality repair shop. The other frustrating part of all this is not having the proper tools for the job. In most cases just having basic hand tools will be sufficient but there are certain tools you WILL need. A really good torque wrench is mandatory, in fact two of them, one in foot pounds and one in inch pounds. You can rent those but I wouldn't trust rental torque wrenches as far as I could throw them because that's probably how they have been treated. Remember Kawasaki's use metric fasteners and even their screws are special. You need a couple of JIS screwdrivers or risk untold grief and damaged screws. Buy them!
I was told a long time ago that lack of knowledge breeds frustration and frustration leads to anger. If you get angry the motorcycle wins! It doesn't want you messing with it. It likes being left alone. Get the knowledge which gives you confidence and dig in. Will you makes mistakes along the way? Certainly you will but don't try to cover them up or look the other way. Just start over and do it right, generally by the book and it will all work itself out. Lord knows there are lots of guys here ready to offer assistance. Good luck now get out on that field Rudy!!!
Rick H.