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That does make perfect sense. I was thinking that oil starvation would have caused further scoring on the pistons and also heated the main journals. The lower cylinder walls did look like they might have had some rust pitting at some point.
Is there any reason that it would take out the top rod first, or is it just the luck of the draw?
Well, the water that is drawn in by a bad/missing lower seal is actually pumped up to the top crankshaft bushing through the recirculation system, then it makes its way into the number one crankcase.
Like Frank says, you better pull that exhaust cover as well, especially if you are going to invest in a new/used crank and rod. Those bores look pretty glazed/rusted over, which might explain the compression variance, but again, heed Frank’s advice and check that head gasket/surfaces carefully. This situation may be a combination of water intrustion and someone thinking these engines can run on a lighter oil mix due to "today’s improved oils".
Be sure to measure the bores, then examine them closely after honing to ensure there isn’t excessive rust pitting.