If you are stopped on code 11:
U4, pin 13, 5.5V instead of 9.5V. <- ignore, it is wrong but because the multiplex is most likely wrong.
U5, pin 13, pulsing <- problem with U16
U9, pin 1, .5 V instead of -24 <- problem with U13
U9, pin 2, 1.3 V instead of -24 <- maybe ignore because of gate bias float otherwise U12.
U9, pin 14, 5.5 V instead of -24 <- problem with U13.
the most obvious error is the last one at 5.5V. I had the same thing when I had a bad U13. Look at U9 pin 9. Try the ground and +5 trick with a jumper and see if you get the correct output. If you do, then one problem is U13.
By the way, does it look like the caps were replaced on the digital supply? Could have been enough leakage to take out a chip.
When the unit stops on a code, it should halt the switching. I haven't tried it, but when stopped on 11, hit the hold manual button and see if the pulse goes away.
If it was my unit, I would swap out U13 first and see if symptoms change. The boards can take a lot of abuse. I use one of those spring solder suckers on the bottom followed by braid on the top. I also have an ice-pick like tool in a screw driver handle with the tip bent 90 degrees about 5/8ths down. Once I suck the solder and push align the pins in the holes, I pry with that tool like a lever. No problems so far.
U5 Pin 13 is strange. That is driven by Pin 11 and you can also test it by grounding and jumpering to +5.
It is not unusual to have two bad LM339 or latches. Part of the problem is they all go around the same time. The other problem is that you don't know who was in there before you. Two of the boxed I had came with probe dimples all over the place.
That table on 8-51 should be your guide when it is stopped. You can ground the multiplex, skip the code 11 getting to code 10 and then try looking at the pins from table 8-B-4 again to see if U13 or U16 are wrong.
This is developing into one of those very satisfying experiences when you fix it.