I have two preludes. Both are 99 year and one is a base model and one is an SH. I thought I would write this up so people searching can find the real solution and hopefully solve it.
Both of them had water leaking in to the trunk. That is a simple fix.
Take the inside of your trunk apart so you can get to the taillights.
Take off your taillights and replace the "gasket".
The other option would be to clean the openings on the car real good. Get rid of all the dirt on the body of the car and clean the old taillight gaskets also.
After the cleaning simply put some silicon sealant around the outer edge of the gasket and put it back on. Let it dry for a while and run a hose around it.
You should now have a leak free trunk.
The second leak that annoyed the hell out of me was the leak on the font passenger side floor. This is what I did to fix it:
Make sure it is WATER and not antifreeze. Antifreeze means your heater core is bad. If it is truly water and it only leaks when it rains, here is your problem.
Now my SH does not have these clips and does not leak. My base model does so I'm not sure if all base models do. I'm assuming so.
First you pop your hood.
Next take off your wiper ARMS with the 12mm socket. (i think, i did this awhile ago)
Next you have to pop off that plastic cover that runs the whole width of the car just under the windshield.
That can be tricky. There are many clips underneath that you have to pinch out. I used a needle nose and had someone kind of hold the plastic up so it wouldn't fall back down.
You should now see something like my picture below. There should be many white clips that that plastic cover went into on top. These clips in fact are where it leaks. If you notice in the pic that the clip above the air intake for the car is not there.
Now you could get new clips and replace them but since I broke my plastic cover and couldn't clip it down there I took out the clip and filled the hole using 3M Window Weld (Nasty stuff!) and made it leak free. For most people. Buying a new clip would probably work. I noticed all of my clips were loose and I'm assuming that's why they leak. If you get a new clip make sure its snug! If its not you could probably get some silicon sealant and put it on around the edges and then snap in the clip.
Now after you have gotten a new clip or plugged it I would drill out the drain hole. Mine was rusty and plugged up. After drilling I shot some paint on it so it wouldn't rust as fast. To be extra safe I glued a rubber hose on the drain hole using my 3M Window Weld (I think that's the only stuff that would work for gluing rubber to metal) to make sure the water drains away from the intake opening.
Now go inside the car (that i had complete ripped apart) and take out your blower motor. There are 3 screws holding it in. 1 is very hard to get to if you have big hands. There should be water in the housing that you should dry up before moving on.
The pic below just shows you there are 3 screws and what it looks like for those who don't know.
I also replaced my cabin filter or AC filter as some call it because with the blower motor spitting water at it, it got moldy and smelly when I turned on the air.
Now with everything fixed but still taken apart, run a hose on the top passenger side of your windshield and let it leak down. Keep an eye on the clip that was leaking and if it is not pouring into the intake opening you should be good to go! You can put everything back together.
I ripped apart my car because of the mold. My carpet pad underneath was completely ruined. I ripped it off, shampooed the whole carpet and had to rip off the rubber pads glued to the floorboards in the car. It gets wet under there too! From start to finish it took me over a week to get completely dry. It is a MAJOR job to gut the inside of your car but I would do it if you know how.
Also the pic below shows under the back seat it was rusted like crazy! What happens is the water leaking into the trunk sloshes forward into the back seat! These preludes are horrible with water leaks like that. Everyone I've seen has had water in the trunk.
I'm doing this write up after waking up and with my girlfriend talking in my ear so if something doesn't make sense just ask and I'll get back to you. If anyone wants to add something feel free. Hope this helped.
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