OK... the leak appeared to have been coming in from the firewall area. The dealer pointed out that I had fed my aftermarket amp power cable through a rubber seal in the fire wall, but didn't use any sealent around the edges. Apparently this enabled water dripping from the windshield into the engine compartment to enter the small hole and find its way down to the floor. The funny thing is that the hole has been there for 18 months yet I know for a fact it did not start leaking until a week or two ago. In any case, I sealed the hole up and am carefully monitoring the condition.
The black mold smell has gone away, and I sprayed the mold with Lysol disinfectant. Hopefully it will kill the spores. The carpet is dry as of right now. The first car wash will be the real endurance test.
Grant