eh... great. Well not to repeat the whole shibang again and again, I'll start with adding a few search words since my search was a little time consuming so here goes:
fj80 leaks windshield slits water drains windshield gasket wet passenger floor wet carpet water logged.
Okay, now here is what I found thanks to the entire crew.
Moonroof Drains:
What:
two holes in the front corners of the recessed area in the roof around your moonroof glass that drain down into your rocker panels on each side of the truck
Test:
Pour water down holes and observe if the water comes out of the rocker panels *immediately*. If not, clear them out.
Fix:
Pull round rubber plugs under rocker panels and do the ones near the front wheel wells. Clear holes with some long wire. There are two holes at the frnt and 2 at the rear. Do all 4. The rears exits just aft of the rear wheels and the frnt flush into the panel just aft of the frnt tires.
Drain Slits:
What:
small slits in the rocker panels that can clog with dirt causing water to stay in the rockers. They are spot welded together for the rocker to floorpan. On these flanges, there are three upsets (Instead of being flat, continuously in contact flanges, there are these upsets, about 1 to 1-1/2 inches long). Plugged slit drains in the rocker drain tubes cause the tube to back up.
Test:
Pull black plastic plug that is in the bottom of the rocker, about 4 inches aft of the fender-to-rocker seam. monitor the upper area to see if you still have water issues.
Fix:
Use zip ties and clear each of the three upset/drains.
Hood Rubber Seal:
What:
Rubber seal at the rear of the hood was worn causing build up in the gap between the hood and body then flowing over the seal dripping down to three wires coming from a relay that are fed through the firewall with a useless rubber gasket sealing it.
Fix:
Replace.
Quarter belt moulding:
What:
Moulding which clips into holes in the quarter just under the window. clips are sealed with foam discs, which may be damaged. If you look on the left side (jack access area) and look up inside the quarter towards the bottom of the window you will see the clips coming through the body. It's the same setup on the right side.
Test:
check the well for water and pull the jack out to see if it is rusting.
Fix:
Replace
And an entire excerpt:
"The below is my solution and steps to assuring a leak free Cruiser:
1) Check your moon roof tubes for any blockages. Pour some water down the tubes, if the tubes back up with water into the moon roof channel and do not allow the water to drain, you will need to get an air compressor and blow out/clear the clogged tubes with forced air. If the air is not working, get a metal coat hanger and untwist it and make it into a long metal rod. Take the rod and push it down through the tubes to clear or push out any remaining debris or blockages, then use the air again.
2) Check for any drainage problems with the doors. Pour or squirt water onto the doors when shut, then open the doors and feel the bottom of the door panel. If water is coming out from behind the door panel, then the drainage holes in the doors are clogged. Use a pick, flat edge screw driver or other means of removing any debris from the door drainage holes. You may also want to remove the door panels and suck out any other debris that may be lying inside of the doors that could potentially or will only block the drainage holes again in the near future. Test once reassembled by again squirting/pouring water onto the doors.
3) Once the moon roof tubes are cleared, check to see if the tubes are draining water onto the ground. The rear tubes exit the body and will drain any water onto the rear mud flaps and then onto the ground (or if no mud flaps, directly onto the ground). These are the easiest to check. The front will drain out of a small slit on the back side of each rocker, towards the front of the vehicle. The driver's side slit is obscured by the catalytic converter shield while the passenger side slit is in plain view.
4) If there is no water draining from the front rocker drainage slits, but water is going down the tubes, then the water is only collecting inside of the rocker cavities.
5) To remedy front moon roof drainage problems, as mentioned previously, there are (4) black rubber grommet plugs on the BOTTOM of each driver and passenger side rocker. These grommets are found or seen if looking at the underside of the rockers and above any mounted running boards or sliders. Get a pair of needle nose pliers or a pick, and you want to remove the FIRST rubber grommet closest to the front wheel on each rocker. Once this grommet is removed, if your rockers were retaining water, any collected water should and will drain. By removing the 1st grommet on the underside of each rocker, this allows any water to drain as quickly as it enters the front moon roof drainage tubes, rather than trying to flow through the very small & restrictive factory slits in the rockers.
6) Test for front water leaks again by pouring or squirting water down the moon roof tubes. You should not only hear the water draining down the tube, but now also see it coming out of and flowing freely through the first holes in the bottom of each of the rockers. The water should flow as fast as you are pouring it into the tubes.
I have tested this over and over while letting the hose just pour water over the moon roof and doors, and to date, the findings, preventive maintenance steps and removal of the rubber grommet plugs under the rockers have eliminated all of my prior water leak issues.
Check the bottom drivers and passenger corner of the windshield, especially if it has been replaced. I found that water leaked in between the rubber gasket and the windshield from the outside, went under the glass then came back up on the inside of the glass between the gasket and the glass. From the FSM, there should be sealant between the rubber and the metal frame AND sealant between the glass and the rubber gasket.
I added a bead of black silicone between the rubber gasket and the outside of the windshield all the way around it. I haven't had a downpour to test if this has totally stopped the leaking, but after washing the car I can not see any water leak from there anymore. This also caused the inside channel next to the drivers and passenger seats to fill with water and soak the carpet on the floorboard. The channel on the driver’s side also carries a larger wiring harness, so that was another major reason I wanted to get this fixed ASAP.
If you have this windshield leak, what I noticed was that the rubber gaskets in the bottom corners were dusty/dirty. Meaning water had brought dirt in and when it dried only these areas were dirty. The rest of the gasket was shiny black and not dirty (for the most part)"