I would start by verifying continuity of the 4 connections highlighted in the picture below.

U16 (resized).jpg

The second thing I would do is clear the holes for the external battery connector and bring the wires to the top side of the board.

Unlikely, but running wires under the board is not a best practice as you can end up with a shorted wire that isn't visible.

Please verify continuity between these two points ...

U15 (resized).jpg

That's probably correct, I actually got a little disoriented between solder and component sides of the board, as I suspect your issue is going to be connection related. You were actually reading thru R38 (10K) with that measurement

You do.

The U15, U16, U17 area is where your direct switch controls reside, this is why you typically see corrosion damage effect the diagnostics operations first, and why I'm having you evaluate continuity in this area of the board.

Here is a larger area of the unpopulated component side, this should come in handy in evaluating the connection points in this area.

unpopulated (resized).jpg

I'm going to be selling a new WPC89 MPU soon, but I don't think your issues justify a new board at this point.

Yes, these four resistors (R35-R38) are all tied to a common point (+5VDC)

This wont effect your diagnostic switches, but will cause your game loose its settings when you turn the machine off.

Actually...This connection doesn't matter since you have no battery holder. the only two points here that matter are your Bat+ (5V) and Bat- (Gnd) points where you are tying in your remote holder.

They would, the corrosion really doesn't look that bad but the areas you cant see seem to always bite you on the ass. You may want to get with Chris https://pinside.com/pinball/biz/directory/1033-chris-pinball-repair he comes highly recommended and will repair this type of damage.

Just for kicks, could you double check those four resistors R35 to R38 (where the fresh flux stains are?) Component side looks like it is solder-starved, the other side looks like there is some potential solder bridging between two of those resistors. Could also be some burned traces. It definitely caught my eye.

Good eye. Its difficult to tell on a populated board, but I believe the points you are looking at are your pullup resistors at the outputs of the LM339's.

Pull Ups (resized).jpg

Anythings possible, but would be kind of far down on my list of things to check. You wouldn't happen to have a logic probe would you?

Just for giggles, what happens when you disconnect J205?

Here is the functional diagram and theory of operation for the are of the board you were working on. I highlighted the 10K resistors in the simplified schematic so you see what point in the circuit you had been working on. The line I put the red X on doesn't exist, its an error in the drawing.

Dedicated (resized).jpg

Since the dedicated switches are constantly active, you should be able to make measurements at point B with a voltmeter. These will be the 4 points I highlighted in post 3, U16 pins 1, 2, 13, and 14

Why screw with batteries?
NVRAM is the only way to go.

Solderong a battery pack is a lot less scary than changing a chip( on the games that are not socketed of course) for myself and others who dont have the skills

I still think you've got acid on the board, perhaps way down under that chip? Take a hard look.

John

Could you post the location of said dumpster? Just kidding you will get this working, just step back and take a deep breath.

These traces are not good. They need to be properly sanded down to bare copper (you can't, any abrasion will destroy them, they are no longer viable) and re-tin and seal them.

There's not much damage there, certainly fixable. But the way it sits now is not good. All the darker green areas of the masking are no longer viable, and need to be properly addressed. Running jumpers is an option, but all that dark area will spread if not COMPLETELY removed.

--
Rob Anthony
Pinball Classics
http://LockWhenLit.com
Quality Board Work - In Home Service
borygard at gmail dot com

I'm starting to think that there may be a break in the run carrying the +5V pullup; please check the points listed in the picture.

Missing Pullup (resized).jpg

If the above checks out take a look at the +5V reference for the LM339 comparitors, if this dashed yellow line is broken (likely at R35) it will cause unpredictable behavior as there will be an open connection to the comparitors. All points circled in red should be connected to +5VDC. (U16 pins 4, 6, 8, and 10)

5V Reference Voltage (resized).jpg

Light bulb is burned out

Unfortunately this statement is completely true; the first four points I had you check are obviously corroded and if not properly addressed, the connections will break, it's just a matter of time.
(https://pinside.com/pinball/forum/topic/help-swapped-to-external-battery-holder-and-game-going-nuts#post-3646101)

Send the board to Dayhuff or Borygard to get taken care of. It will be about half the price of a clean working original WPC board. Don' t forget to ask for NVRAM to be installed as well.

If you do any other soldering to the board, do not solder on the top side of the board as the heat with the corrosion will eat of the pads very quickly.