some info here at a local prelude club forum
VancouverPreludeClub.net ? View topic - stupid water!!
I've had a similar problem on my Prelude. It was the sunroof drain hose plug. The black rubber piece that connects the hose to the car at the bottom of the trunk on the sides. Somewhat above and behind the real wheels but in the trunk. You should see them if you pull your trunk carpet out.
The other issue was the plug in the trunk near the spare tire. I removed them so the water can drain right out if water should start pooling in that area.
I also made my own rubber taillight gaskets with some foam that I bought from Michaels. I forget the brand name but I remember the label was blue and had a penguin on it. This is the closest one I could find:
http://www.michaels.com/M10390268.html
At the time, only the Langley location had the item when I purchased my rubber foam gasket thingy
Good luck,
Mike