...and the solder work. Hi-res photos of both sides of the board.

This is why it is highly suggested not to shotgun problems.

The game doesn't know if there's a ground short or not. All of the rows are pulled high by resistors and if any of those rows read low then the system surmises you may have a ground short. So while a short in the row will cause the error the system not seeing 12 volts on the row for other reasons (board problem for example) will also cause the error.

My guess would be that after all of that work you've lifted some traces or destroyed some pads/through-holes. Thus the cpu won't see 12 volts on the row and will report the error. On a board with heavy alkaline damage it's almost impossible for even a pro to pull chips w/o doing damage. It's much easier to troubleshoot and fix though if you catch it before the new chip or socket is installed.

This is not directed at the OP, but for those reading that haven't learned this lesson the hard way: don't shotgun stuff since you'll more than likely compound the issue. The switch matrix is very easy to troubleshoot with a logic probe. Especially don't do this on an alkaline damaged board since the alkaline gets under the copper and eats away at the glue attaching it to the board. Traces and pads are already half-off before you even start soldering.

A heavily damaged board should really be sent out to one of the board guys; whatever amount of damage you see there's four times that much hidden under IC's and other places, and they will know where to look. I've had boards where if I lightly pulled on the resistor leads they would separate from the resistor. There's really just a lot of stuff to check on battery damaged board.

Make sure you check the through-holes for connectivity from one side of the board to the other.

A lot of people use nail polish and I don't see any problem with that. I use glass paint (see my soldering guide--I think I covered that) to match the solder mask color since my customers in my non-pinball day job like pretty boards. Personally I would otherwise use conformal coating since you can still solder the joint without removing it first; it melts at soldering temperatures.

In any case I would try to keep the protective coating off of the joints. The conformal coating just gives you a little more leeway.

I don't pull resistors unless I can't reflow the solder on the joint. I do though go along and put a pointed solder pick under every lead and pry up slightly. You would be surprised how many will break loose if there's much alkaline damage. It's also really fast just to run your loads down a row of resistors and check their resistance.

The alkaline damage treatment you did looks good.

I will admit this is being picky (and probably not a functionality issue), but the joints on the four resistors below the R27 label look pretty dull (corroded). I would hit them with a fiberglass pen, add some flux to both sides of the board and see if you can reflow the solder. If you can't (again being picky) I would pull them, clean the area and install new resistors. Or you can just ignore me.