You replaced both J120 and J121 connectors correct? Also J115 can also burn, this may cause some of the same issues you are describing as this connector brings in power to the board and then back out. Check that connector too.

You can swap the connectors for J120 and J121 around and see if the string of lights that don't work move. If you swap J120 and J121 and the backbox string is still out, the issue is in the connector wiring or lamps in the back box. If you swap J120 and J121 and now several strings on the playfield are out, then look for board issues (header pins, traces, broken plated through holes, blown fuses, etc.)

The manual towards the back shows what wire color goes to which pin on J120 and J121. Be careful when counting the pins because the pins on the board are numbered right to left.