I have a 1999 and aftermarket deck. Is the mulitplexor replaced yet? I would wait to do that job until you do more research. When the new deck was installed, the auto dim/illumination wire may have been connected to the orange wire in the harness. For some reason, 98-02 Accords don't do the auto dim thing (when you turn on your headlights, the deck dims a little bit) and will cause lighting issues. When I installed my deck, I connected that wire and had a ton of issues with interior lights and brake lights not working.
I don't think it's a multiplexor issue at all, but then again, if it's fixed you could try reinstalling the deck without attaching the orange/white illumination wire.