So, removing everything that the J1 connector connects to still freezes it up? Are you sure all the wires in J1's connector aren't shorted out to something?
Can you leave just J1 and J4 (left side connectors on) and take the J2/J3 (right side, switches) off? What happens then?
Since you get 3 dings which equate to 3 flashes, U10 would be the culprit - but nothing that plugs into U1 goes to U10. However, the dip switches and switch returns all go into that, so perhaps there's something on the playfield switches, or the cabinet switches, that is shorted and causing a register on u10 to be messed up, which would certainly cause the mpu to stop where it's stopping.
Pull the GI and solenoid fuses out, because it will still boot at least up until the 3rd flash (solenoid is needed for the last flash on bootup) - but this will take those 2 sources of stray voltage on the playfield out of the mix.