OK so there was an issue coming from undoing the backbox wiring to get it downstairs. Some times while playing the game will just reboot. Or sometimes the audio will reboot. Once the DMD just displayed an error at bootup.
These issues I have mostly traced down to a single connector that feels a bit loose. It is a touch flimsy and I am not sure if it was this bad before disconnection, but it is the first thing I attend to if/when something does go wrong.
I had a guy over to help move the Royal Flush and he mentioned the connector, described it perfectly, and apparently they are notoriously bad. So add to the todo list:
13) have that power/ground connector rebuilt!
I am hoping that will solve the issue. It's very rare and erratic (oh, THOSE kinds of issues...) but at least I have a good starting point.