You bought a nice low speed trail bike, that is very easy to learn on. It can be modified to do lots of things better than it does now. There is one area of concern when you say something about it not having as much power as you would expect for a 200 cc bike: In stock form and running at it's best it probably will still feel that way if you are comparing it to ANYTHING that is of the racing variety.
I have had good luck with any of the aftermarket valves and pistons if you keep the compression stock, ditto with the cam and carburetor. Vesrah used to make decent valves, which were inexpensive and a good motorcycle or automotive machine shop can recut the seats and shim the valve springs for you. You should have the guides replaced or knurled to take out the play and center them again.
The good news on the crankshaft is that if yours has a stock bore it probably means it doesn't have as much time on it as it would take to wear it out. Thus if you are rebuilding it to stock specs, it can probably be used as is, taking into consideration the checkup that Srad suggests.
Pricing out a bag of oe parts that came a year ago with a 200 I ended up with, I don't think you would have any trouble doing the top end for under 500 including the machining.
You asked about checking valves, and my favorite test is before I disassemble. I would have set them first and then done a compression test, carburetor off and kick it over a few times until a rapid rise on the gauge stops. it it seems low, i take out the plug and put a few squirts of oil down the plug hole and kick a few times to spread the oil and blow out some of the excess, and hook up the tester again. If I see something like a 20 lb plus rise in the reading, I know that the rings are probably the biggest part of the compression loss. Since it is only two valves that are not outrageous I just usually plan to replace them, as the stellite coated ones that Honda uses don't lend themselves to turning them. In no case would I put it back together on the stock piston, and boring costs so little once it is apart, I would just plan on that. Even a cylinder that is still within spec is going to be close to be over the limit. Your chances of getting it concentric again and seated good are about as much as getting on an airplane that is going to be hijacked.
So if it were mine I would put in a new piston and rings, new valves, all the gaskets etc, and probably a cam chain.
The process is different if I decide I want to change cam profiles, springs, carb etc.