Has anyone had a problem with their S2000 leaking around the windows, windshield or top during hard rain? Also, to get the best seal around the windows, is it better to roll the window up before or after shutting the door?

 

You can try shin etsu grease on the seals

 

i agree, add shin-etsu grease to all of the seals. They are likely dried up due to age and have shrunk a bit.

 

I had this same issue. I used the above mentioned grease and also checked out the rubber ends on the corners of the softtop in the front. I got water leaking in there. I removed the ends (1 screw if each I recall) and checked things out. I used a tiny bead of RTV Silicon once I cleaned up the area and dried it. Not a leak at all since.