One Solution to Same Problem
I bought a used 98 several years ago and had the same problem—the driver’s floorboard would be wet after it rained. It has a factory installed sunroof/moon roof and I also suspected it as the source of the leak.
I got down in the floorboard and noticed the bottom/base of the floorboard was wet but as I moved up the slant toward the firewall, it was dry. I had someone spray water on the windshield on the driver’s side and noticed water dripping from some control cables/wires that came through the firewall through a factory installed grommet just above the brake/gas pedals. I have included several pictures of the grommet involved.
But it wasn’t a Toyota issue. My 4Runner was previously owned by a college student who had obviously installed an amp and they ran the power wire through that grommet. In the process of installing the wire, they pulled the grommet away from the lip of the firewall at the very top of the grommet (the 12 o’clock position) and then forced the wire through. This caused the grommet to lose its water tight seal and the wire became the carrier of the water.
The water/rain would follow its normal path down the windshield and firewall but when it reached the grommet, rather than flow around it, the water would follow the amp’s power wire through the grommet and firewall and into the cabin. It would then drip off the control cable/wire onto the floorboard.
The wire was still in place when I bought the vehicles as they just cut it and left it in place. I pulled the wire out, pulled up on the grommet to reseat it and I’ve had a dry floorboard since.
Another suggestion regarding the blowing of compressed air through the drip tubes of a moon roof/sunroof to unclog them. In doing my research for my leak I read were one poster advised not to do that because you can dislodge the small plastic tubes from the sunroof/moon roof then when it rains, all the water flows into your headliner. They suggested taking a small wire and pushing it through the drain tubes to unclog them.