The drains are back in front of the rear tires. One on each side. Look like this
View attachment 29074
The convertible top is designed to channel all the water flowing down it into two large pockets under the rear quarter windows, where these drains are. If they are clogged, the side channel under the door fills with water. Often times it comes out in the rear floor, but if the car is parked with the nose downhill, the water can flow up the channel and come out in the front area. If you pull up the door sill and peel back the carpet, you'll see it's wide open int he front.
Clear the drains with a coathanger or compressed air. There's couple rubber plugs in the floor you can pull to help the water drain out in the meantime, and just peel back the carpet and let it dry. You can also get in the car and have someone use a hose on the exterior and see if oyu can ID leaks.
The header seal around the windshield is also another source. Water flows around the windshield and actually runs down a channel in the A-pillar seal on the inside of the window and then crosses over and dumps at the front of the door jamb. Sometimes this seal get filled with leaves and detritus in the channel, which causes the water to dam up and spill over in the area where the mach 460 speaker is. It then flows down the inside of the dash area somewhat out of sight onto the floor. The 01-04 seal is redesigned and compatible with the 94-00 cars, but you need a few seals as they all work together.
I had the same leak in my '00 convertible. I cleared the rear drains, as well as cleaned the inner channels on the header seals (and found leaves). That seems to have done the trick as it's been several months now with no leak problems. I park the car outdoors, so it's always in the rain.