As I said, I don't think guide sealing will affect the blowby. As far as the uneven wear on the second ring, I believe that will be normal for a modern ring that has a taper face for quicker break in--in other words it is not fully worn in until the face has worn enough to be flat. Usually the top ring is ground with a barrel face which is higher in the middle.
Your ring gap is great and the piston clearance is just right to run without any danger of seizure.
You did measure the piston at the largest diameter of the skirt?
I assume they necessarily honed the slightly excessive clearance to correct the waviness you saw at the second teardown.
It sounds like the machinist would have caught this condition if he had used a positive expanding hone as a final finishing operation. The faster abrasive brush type tool will hide the irregular surface where a positive expanding hone will show it up and correct it.
