Update.
It's running and no more blow-by!
There a minor amount at idle that I'd consider it normal. It's gone within a few inches of leaving the tube. It's not like the 20 feet it was doing.
I ended up replacing all three pistons with new rings. When I checked the ring end gap the front and middle cylinders were at the minimum .008". The rear messed up cylinder was at .016". Well within the specs. I probably could have just replaced the rings on the front and middle cylinders, but I figured since I'm in there it will all be renewed.
Everything went well during the rebuild less breaking one of the rocker manifold studs. It shear right off as I was torquing the assembly down. I was able to get a piece of 8mmx1.25x100mm all thread from the hardware store. I cut it down to match and off we went.
I'm still not 100% sure if the seal on the end of the air filter is sealing to prevent the dust from entering the engine. I'm going to periodically pull the intake hose off the manifold and inspect to prevent this mishap from occurring again.
I was also able to repair a leak on the steering ram. The seal at the end of the ram body was just riding the rod. I didn't see the seal until I removed the ram from the tractor to start working on it. It was an easy fix after I cleaned things up.
At this point all is good. I ran it hard for about an hour to help break in the new rings. It ran strong and didn't lug like it used to. I guess when you're running on three cylinders and not two, you have more power. The knocking is gone. The smoke is more gray now when you get on the throttle and clears up fast like it should. It was puking more black smoke before between the low compression in the one hole and the dirty intake and valves.
Total cost for parts was around $700. The piston/ring kits are $170 each. The gaskets add up fast too. I also spent a little to upgrade my tool collection as well.