Sounds like you need to resolder the male pins on the MPU board for the boot up issue.

You could have one display causing the issue. Mainly this comes from a common pin used on all the displays. Try disconnecting all but one display. If it lights up correctly, keep adding one.

Would really help if you told us what game you were trying to use this in. Some multi-ball games will not come up after the 7th flash because it does not see all the balls.

CPU interrupt problem? The four lights lit up is probably the decoders parked at input 0000

can you check U10 P18 for the zero cross detection? Should be pulsing at 120hz. If all you have is DMM, just make sure it is not stuck at 0.00 or 5.00vdc.

Have you got original gas displays or newer led segment displays?

A missing digit is easy to trouble shoot. The 1,000s digit is J1-4 on the MPU. The connector is bad or the wire is open or shorted. Could be a bad display or more likely a problem at the connector on the MPU.

so maybe a broken wire since you've redone the connectors (or just bad job doing that). Tone out the wire from the connector back to the displays.

Sorry for opening this old thread.
I have been working on a Stern MPU-200 board (nine ball) and had the same problem, 7 flashes but locked up before attract mode.
I noted the VMA (valid memory address) signal pin 5 on the 6800 was not pulsing after the 7th LED flash.
Also the MPU LED was not illuminated dim after the 7th and the PIAs were not outputting (no displays on pin).

It turned out to be broken (cracked) pins on Eprom's U1 & U2. I assume the same problem can occur with old corroded IC sockets (or being pushed and pulled over the years).
I don't normally fix pinballs but I would assume this is a more common problem than is realised.
I have to replace the eproms later but did a temp repair to prove it.
Thanks for your thread as it was one of the few that had this subject.