I just tackled my firewall leak last week with info from this thread. Couple notes:
On the OBS trucks, you can still get to the old vent access mentioned in an earlier post on the passenger side, but the drivers side is covered by the e brake bracket. If you remove the cowl cover you can snake a small shop vac hose down there and clean out both sides from the top. It definitely needs to be done.
All the seam sealant in my cowl vent was crusty, and lots of it had fallen down into the drains. I sucked it up with the shopvac. I am pretty sure that is where my leaks were coming from. I cleaned rest of sealant out, por 15ed the seams and applied 3m automotive seam sealant to the whole area.
I didn't mess with my heater box, because it was unmolested from factory at this point, and I couldn't see where any volume of water would get to past the cowl seal. I had water pouring into the passenger floorboard when driving in a rainstorm, even after replacing the windshield.