LED 3 being off, not likely nothing to do with coils not firing and inserts not working if the game is booting up. With power off measure the resistance of R6. It should be measuring around 800-840 ohms.

With power off, I would reseat the big wide ribbon cable at the MPU, at the interconnect board, and at the driver board.

Sometimes they come partially unplugged when folding down the backbox.

Just like any other ribbon cable, the contacts inside can be become spread out from the cable being removed multiple times. If it happens again, I would replace it. https://www.marcospecialties.com/pinball-parts/RC00103-1

Do you know for sure you installed the single board LED the correct direction? Just like a diode, it must be installed the correct direction for the LED to light up.

I think you can hold another LED on the board connections to see if it lights. If it doesn't, can turn it around. So you can do this without removing the board, just as a test.