I don't know anything about the Yanmar engines except mine have worked well without problems. That said the older engines with wet liners would be beneficial in your case. I rebuilt my old 450 dozer with new pistons and liners rather easily in a day or two.
Any possibility you can salvage the bore by honing?
I don't believe the bore can be salvaged. Given that it is a wet liner, I feel fairly confident that I could replace it myself. Since the head is already disassembled and needs work, I'm planning on disassembling the lower end this weekend to take both a machinist. I'm hoping I can get by with a replacement sleeve, rings, bearings, and having the other two cylinders honed. Should know more next week. Provided the block and head are not cracked, this should be a relatively simple rebuild.
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