I have just recently bought a 1999 eclipse spyder gs. I too found out, the day after I bought it that the roof leaks pretty bad. I work at a construction company so I have dealt with leaks in things before. so, I went to the local hardware store and picked up some 100% silicone sealant and started squirting anything that looked like it could leak. I can put a pressure washer to it now with no leaks!
I have the same problem with mine...
Generally around the window gaskets...
I am not sure how to use the sealant, since it is a convertible...
Can you explain what process you used to seal it..