Well, it took me several weeks, but I've finally fixed this issue. I had swapped bulbs, I/Os and the MPU and verified all plugs and connectors were snug, but to no avail. My last idea - to swap out the button harness - proved to be the solution. Turns the old harness had some poorly spliced wires (although I'm not sure why) and a couple of spots where the insulation appears to have melted to the point of exposing the wire underneath.
Whatever. It's fixed now. Thanks to Ohio Gaming for the harness swap and thanks to you guys for the ideas and encouragement! Consider this topic closed!!