Honestly, I never saw any real difference between the early head / piston combo and the later combo when I changed mine. For power, IIRC, you would use the early pistons and the late head (again, IIRC, the late heads have a smaller combustion chamber).
I definitely advise contacting Jerry for parts. Jerry really took good care of me. As long as you are dealing with Jerry, don't forget the (4 maybe?) small coolant hoses that go from the intake manifold and molded heater core hoses. Now's the best time. Dennis
On your cylinder pitting. If it is below the lowest RING TRAVEL, you shouldn't have a problem. The piston will obviously "touch", but the rings are what you need to be concerned about.
Here's what you do: Measure from the top of the piston to the bottom of the lowest ring. Now measure down from the head surface of the block 3.7", and add the measurement from the piston measurement. If it clears the pitting, you have no problem at all. If it is in the space for the lowest (oil control) ring, you might still be okay. The second ring, the "scraper" is what you need to be most concerned about.
You can probably put it together and be okay. A few years back, I did some work on an engine for my kid brother (the machine destroyer). This was a horizontally opposed Kohler industrial engine, it had been sitting, and was locked up. On removing the heads, both cylinders were pretty rusty. At least one had scales on the cylinder walls.
I told him it would probably need bored and new pistons and a replacement engine might be cheaper. He asked me to try it. I ran a hone through it with the pistons still in it and at bottom of the stroke. I put the heads back on (with the old gaskets), changed the oil, and it fired up. It ran without smoking. I ran it for a half hour and still no smoking. To the best of my knowledge, he is still using that engine (it's on a small stump grinder). GHope some of this info is helpful to you. Dennis
BTW, increased compression ratio will probably not affect emissions output.