So you have three parts where you can adjust the window seals:
- With the roof completly down, you can access a seal alignment screw in the left and right part of the windscreen. (You tighten it to make it go outwards)
- After you align the one above, you can align the seal on the first shell by unscrewing 5 T20 screws and moving the seal (to the left or to the right as you look at it, to the front or to the back of the car).
- If, after modifying these two, you did not manage to make the leak go away (if you have a leak at the front, redo step 1 & 2, if you have it between seal 2 & 3 you continue with this step). Above the "small window" there are 6 T20 screws that you can play with as well, you can align that seal as well.
From what I did on my car, I believe only step 1 & 2 are necesarry and you should not change the seal at the back.
+edit P.S: After realigning put a LOT of water on the gaps to check if the water gets inside. (Check on the windows - small & big, on the windscreen and at the pillars that are around the windows)
+edit2: I am fixing my roof this week and i'm going to have to realign my seals as I've moved them a little bit to have better access - i will make some pics for you so you can see exactly what & how to align.
+edit3: You can buy a new seal for the first roof shell, but it costs like 500 euros, just check realoem, maybe you find your "problematic" part