I found that my soft top rail interfered with the hardtop at the channel that the seal sits in. I had to modify the hardtop by cutting off the rib at the back of the rubber seal. When I pulled the old seal out, the adhesive wasn't going to hold it on again. For a new seal, I used some generic foam-rubber door seal material from Home Depot. It tends to compress pretty well.
Before:
After:
I also tried to take some material out of the corners to get the corner seals to fit better, but they still don't fit right. You don't really need them, and the slight increase in air draft is drowned out by the draft from everywhere else.
