Man have I been down that road...
There are several area that is could be...
The cowl gasket often leaks, I recommend replacing it anyway. I don't recommend siliconing the cowl unless you never want to put the windshield down again. You can never get the old RTV off the paint. If you have a garage and can let the RTV dry, you can do a thick bead on the existing gasket and that will give it a new pressure place to seal once dried. However, for $35, I think it is just better to buy new.
This is as good as the OEM
This stopped my driver side leak. :lol:
As for the passenger side, that kill the radio, been there, and it is the air box gasket. To be sure, I tore my entire dash apart and drove in the rain. Found it. I did not think it could be it, because I had sealed that once already but I found out exactly where it was. First thing to check, take the cover off outside, then be sure there is no clogs down at the bottom and best test this by using a hose and be sure it pours out from by the engine. Next, check the other hole, :lol: this is located in the engine compartment, it is right under the battery tray. It is a strait brass pipe coming out of the firewall. This is there even without having AC. Be careful while poking it. Lastly, while putting the top back together, this is where I finally found my leak. See, mine did not leak all the time either, it depended on how I parked, also, how hard the rain was and if I was driving. I found it to be the top seal of the air box, where it pulls up to the sheet metal. See nothing holds that air box up except the screw from the cover going down from the outside. And when it would rain hard, it would go under the plastic outside cover, and then go over the sheet metal edge. Where it should have "dripped" into the plastic box. However, instead it would go under the metal and trough into the cabin. So from there, if it was a heavy rain, it drips on the stereo, and if it was a light rain, it drips down the box, and over to the right and then to the floor.
The fix, well again stay away from the RTV unless you want it to never come off or come off but with paint attached. I instead tried doing a bead of RTV on the outside cover inner lip and letting it dry to make its own gasket. Nope, did not work... to much water runs off the windshield and runs right under the cover and the RTV just did not contact everywhere. The solution, use some foam gasket tape. The stuff from the hardware store that you use in windows and stuff. Cut yourself 4 pieces and stick it to the inside of the grill cover, and be sure to over lap it in the corners. Screw the cover back down (not over tight, the plastic cracks with age) and no more leaks... This took me almost a year to find and drove me nuts almost to the point of selling it and building and beating my Rubi instead....