Spend $20-$30 on a decent micrometer. You will use it many many times. I dont know what the exact # s are. But i know the factory suzuki manual will tell you the cylinder and sleeve heights. Measure them or have a pro check it.
You said that the piston is covering the exhaust port just before TDC but at what degree on the crank rotation is that? Without a degree wheel you cant know if the port timing is correct.
I also wonder about the PC on the cylinder.. It looks great but often PC'd cylinders need redecking afterwards due to the baking heat of the PC. Could your builder have decked too much to compensate for the distortion of the base or head surface after the PC was cured?
Im kind of echoing others here... You need to get very specific answers from the builder to find out whats up. And take it from there. I suspect the cylinder was far from true on either the base, head or both sides and material was removed to square it up.