Hmmm, since you pulled the fuses and replaced and now lights are working one possibility to me are corroded fuse holders and removing and replacing them got a decent connection. You could pull the fuses and inspect to see if they or the clips look dull or corroded. Other possibility would be cold solder on the fuse holders. Flip the board and reflow solder. Another possibility is when you lifted the playfield you could have wiggled the wire harness and there was a loose connection at the board. Pull the GI plugs on the board see if they look burned or dirty. You can clean the connectors on the board for temporary relieve. Also could have wiggled the connector on the board for GI and it has cold solder joints. Flip board and reflow. Either way eventually you'll have issues with those connectors and the pins on the board and the plug. If its just in your home and its working keep rolling. If I were doing it for someone else I'd replace plugs, pins, fuse clips and reflow every connector solder joint on the board. There are many purists who like to keep the incandescents. I'm not. Led's are known for drawing less current and therefore much easier on the old wiring and inserts.