Are you getting 5v on the mpu? Have you repinned the connectors on the rectifier board?

3rd Flash: U8 5101 ram OK (U8 & U13 on mpu-200)
4th Flash: U10 PIA OK (see details for caveats)

https://pinwiki.com/wiki/index.php?title=Bally/Stern

Wow....wow. alltek even in the title and I missed it
Confusing...alltek shows a proper sequence but then says...
"Just a note, Baby Pacman has a little bit of a different Self-Test sequence"
?!

Its almost like all this beer isn't helping my reading comprehension?!

Bump

If this is a new board, contact Alltek for help.

At which point did it give 7 flashes? Did you have everything connected when you had 7 flashes? I would try to connect the strict minimum to the board. The next flash you are missing is related to the PIA and it always possible that something is shorted on the playfield and it is not allowing the PIA to act properly during boot. You have a new board and are repairing that machine which means, it has issues before I assume. Did you verify the dipswitches and made sure they are properly set for Mr Pac man? No switches have been slightly nudge when manipulating the board and are maybe in between 2 sides?

Right now your board stops when trying to test u10. U11 is the exact same chip and can be interchanged, but if a connection damaged or is preventing u10 from working properly, unless identified it would cause the exact same issue. You have to eliminate all possible causes one a time, so start with the bare minimum to boot the board, add another connector and boot again and so on.

5th flash not working is problem with U11.... u10 is the switch PIA, U11 is connected to the displays and the solenoid control. Try disconnecting the displays to see if something is feeding back through them.

You can swap the chips to see if the behavior changes. I wouldn't do too much though as even though Alltek has the lifetime warranty, it might be void if you start to fool around with stuff.

I don't think you're having a power supply +5 issue as the board just wouldn't boot that far consistently if you had. Set the board up and swap it into your Embryon and see if it works there.... advantage having 2 machines for this type of troubleshooting.

Also, it is possible that you're interpreting the normal 'flicker' of the LED at power on as the first flash - if this is the case, you are actually stopping at the 3rd flash which would be the u10 pia having issues instead of u11. These are connected to the switches, so you can remove the 2 harnesses on the right side (j2/j3) and see if it boots farther.

All the part and connector numbers might be different on the alltek, u10/u11 j2/j3 are what they are labeled on bally boards.

Yes, that is likely there is a sneak short in the switches on the coin door or the playfield (probably to solenoid voltage as lamp voltage would likely be ok)
Of course M&MPM also has a display in the playfield so there's the +190vdc floating around in there as well. Lots of fun stuff to check for shorts.

You could narrow it down by pulling the high voltage fuse from the rectifier board, the solenoid fuse from under the PF, and the lamp fuse from the rectifier board too. If it boots with all of those circuits removed, reconnect one at a time and see when it stops booting... the short would be on one of those circuits. Otherwise, you'll have to look at every switch connection to see what else might be shorted against it that shouldn't be. Common culprits in this situation are coil brackets, but sometimes it ends up being something that mashes through a mounting screw that you can't see. Not a fun time, especially on a packed playfield. If you do find it's coils and the drop banks are on connectors you could remove them entirely to take that out of the equation, and would make it easier to inspect the wiring closely. Nice bright light helps here.

This is of course if the board is still working and the bootup interruption now is caused by one of those circuits. If it's just dead the same way in your embryon, it's the board.... possibly damaged by the short. So you have to find the short before you put a working board back into the game, unless you want to sacrifice 6821 pia's with troubleshooting as described in the previous paragraph with the fuses.

Did it ever boot all the way up in the game?

You didn't by chance plug a display connector the wrong way around or off by one pin? This can potentially send high voltage back into the PIA - can burn out the resistor leading to the PIA pin that got the zap.

Alltek Rev D to Rev J:
Bally U7 = Alltek U16
Bally U8 = Alltek U16
Bally U9 = Alltek U7
Bally U10 = Alltek U8
Bally U11 = Alltek U5

Alltek Rev K & Rev L
Bally U7 = Alltek U15
Bally U8 = Alltek U15
Bally U9 = Alltek U5
Bally U10 = Alltek U6
Bally U11 = Alltek U2

Swap U6 with U2. They are both 6821 PIA chips. See if the flash sequence changes with one more or one less flash.
If it's faulty, you can get new replacements from GPE:
https://www.greatplainselectronics.com/proddetail.asp?prod=W65C21N6TPG-14

6821 chips can die on their own.