Quick update on this project. I have ordered 3 new piston assemblies, crankshaft bearings, head gasket, fuel injectors, and some other misc. parts. I ordered everything from Messicks, and I hope to have those things in the next couple of weeks. They had to order a few of the items directly from Kubota.
In the meantime, I purchased some honing oil and a flex hone. Based on my measurements, I'm planning a light hone; just enough to get a good cross-hatch pattern in each cylinder bore. Any helpful hints on this process? The crankshaft is still installed and, based on what I've read, I need to place some rags or other protection over it while honing.