It sounds like you may have a few problems, so you may want to tackle them one at a time.

Have you while in switch test mode removed the connectors to the switch matrix pins in the back box and shorted the pins for each column and row to see if each switch is triggered? That will tell you whether your switch issues are board related or playfield related.

Also, did you just get the pin? Was it working fully before all this started? Did you do any work on it yourself?

Since you have so many issues the first thing I would check is to make sure the Alltech is configured for the right game.
You say the switches register in self test, have you checked the displayed number against the list in the manual to make sure the correct switch is registering?
Double check the solenoid board connections.

Did you do this by pressing the switches on the playfield or by shorting the pins on the board?

So the left outlane switch registers in test mode but not in game?

As for the left thumper activating the sling, does it do this all the time or only when certain other switches are closed, like the drops?

Unfortunately, that’s above my pay grade. But, I agree. Time for a drink.

I think BigAl56 is your best bet here.

I'd recheck the connections on the SDU and also reseat the connectors on the MPU.

Are the female connectors on the MPU original? If so, they may need to be re-pinned if the previous board had battery leakage. That stuff creeps anywhere it can go

That's good troubleshooting, but some of those connectors run between boards. Some connectors carry the data between the MPU and other boards. Occasionally I've seen weird problems due to bad/incomplete data signals that can lead to improper coils/lamps/displays and it all came back to connectors.

For example, the SDU has 4 data lines coming from the MPU to tell it which coils to fire. It's done in binary where 0 volts is "off" and is a binary "0" and 5v is "on" and is a binary "1". so it would look something like 0001 for coil 1, 0010 for coil 2, 0011 for coil 3, 0100 for coil 4 etc. If one of those 4 bits is stuck on or missing, it can lead to the wrong coil firing. For example, let's say the first (right-most) bit is missing (or not putting through the proper 5v) due to bad or broken connection between MPU and SDU. That means when it tries to fire coil 3 it reads 001*0* instead of 001*1* and in turn will fire coil 2 (0010). I hope this makes sense

There's similar systems in place for the MPU to tell each board what to do, including the lamp boards.

One other thing to check: the ground connection on the auxiliary lamp driver board tends to go bad. Might be worth your while to re-pin that connector (male and female sides).

It's surprising how many issues come down to connectors on these games, hopefully you'll find that's the fix here.

When you say four flashes, are you counting the initial flicker the LED makes?
It sounds like it's a PIA problem based on # of flashes, not sure why it would suddenly crop up though. You could try reseating the PIA chips or perhaps try swapping them (U10+U11) and see if that makes any difference. (Edit: this doesn't apply to Alltek, unfortunately)

Bonus edit: I grabbed an alltek board I just recalled getting a while back and it looks like the pia chips are at U2 & U6. Still, not sure if swapping/reseating/replacing them is going to fix it, but I think that might be the next step.

I don't know Alltek boards though, so I'm not sure how much of that info will apply...

I know you said you verified the wiring to the connectors, but have you verified the pin positions for each wire as well? I've re-pinned female connectors and discovered afterwards I had several pins shifted one spot left or right (put one pin in the wrong slot, leading to the following pins also going to the wrong slots)...

If all the pins are indeed in the correct spots, maybe what happened was just a coincidence. First you had the weird behavior with the lamps etc, then this...perhaps the weird behavior was the first sign of a PIA on it's way out, now it's done.

If the wiring all checks out, I'd try swapping the PIAs and see if you get an additional flash out of the MPU (meaning the problem is likely following the chip, if the flash sequence for the alltek is the same as the bally 7-flash sequence)

I think that actually means 3 flashes--the flicker shouldn't be counted. No 4th flash means a problem with one of the PIA chips (U10 on a bally/Stern board, not sure which it is on the alltek--either U2 or U6)...a proper boot will have a flicker, brief pause, then 7 flashes (again, that's how it would work on a bally/Stern MPU and I'm presuming the same for the alltek)...