I have both tops... On the soft top I found that the vinyl wrap that covers the windshield to the targa bars just didn't completely fill the door gap void.
When I installed the hard top it was worse becaue I had to remove the vinyl wrap. What I did was go to the hardware store and bought foam strips that have a double faced edging in them. I found this in the area by the air conditioners. It is used to fill the gap around the windows when the air conditioner is set.
No more problems... I also found that with my hard top (it is a 2 piece) that I had to spend extra time with the adjusting latches getting them to seal properly. I had to trim the outer seal above the windshield corners on the front top to get it to seat deeper too.
I can't speak if this is normal or not because this is the 1st time that this top had ever been on this Samurai so I assume I needed to tweak it in order to have a proper fit.
Once I had done this everything was great. With the exception of the stock tire carrier rattling the back door due to the weight. I fixed this by building a swing out tire carrier and now the Sammy is bone quite going down the road. Enough so that I am going to put the AM/FM/CD player in it soon since I can now have some sense of security with the hard top vs. the open access of the soft top.
Hope that helps some....
Tux...