I don’t know which step fixed it, but I’ve got LEDs lit up on analog 3-4 for both input and output (without being in bypass).
I completely removed both ribbon cables after clearing out the hot glue (?) from the board connectors — the glue gave way pretty easily.
I reseated both ends of each cable several times to remove any possible oxidation.
I didn’t remove the audio chips but gave them a good press all the way around (1 audio on the daughterboard, 1 audio on the main board and and another on the main board).