I have been perplexed at the leak in my Rover since I got the thing four years ago.
Windshield: I sealed the rubber at the top with 3M Window-Weld, packing into the area where the original rubber mated into the glass. After a good summer of blistering hot days, the Window-Weld evaporated? or shrunk, not sure which. I too a plastic Bond-o scrapper and pushed the rest into the remaining seal. Then I put the Permatex Window Sealer in the gap between the rubber and the frame until it filled up to the brim.
Do not drive for 24 hours while the sealant sets up.
To prove out the repair, I bought bottles of rubbing alcohol and poured onto the newly sealed joint. Have someone sit inside the Rover and try to smell the alcohol. If alcohol is not smelled, then that is sealed. The alcohol method is what I used to determine I had a leak on the wind shield.
(A) Window-Weld
http://www.levineautoparts.com/3mwirorise14.html
(B) Permatex
http://www.drillspot.com/products/278234/Permatex_81730_15OZ_Windshield_Sealer
However, The leaks persisted...So it had to come from the one or both of the Moon Roofs.
Using another bottle of rubbing alcohol I poured around the glass (front side) until I saw alcohol draining from the tubes on either side of the doors. Still no smell of alcohol inside the Rover but when it rained I would still get water dripping from the head liner.
I did notice that if I parked at an angle where the driver side is lower than the passenger side, the leaking seemed to stop. To this day I park with the driver side downward.
Well, one day while I ran through a local car wash to get rid of some bird crap, the power spray started pushing water inside the Rover. Ha! I found the leak. It was coming from the back part of the Moon Roof where the glass and rubber seal. Both Moon Roofs leaked in the same place.
So I deduced that when the Rover was sitting on Level ground and one of those torrential North Carolina downpours happen, the water would pool on the roof while trying to drain.
To solve that problem, I would spray Belt Dressing onto the rubber and close/seal the window making the rubber stick to the glass. When the weather is nice for the Moon Roofs to remain open, the sickiness does dry up some and I do re-apply on occasion if I start getting water inside or just because of my devotion to the Rover.
(C) CRC Belt Dressing
http://www.farmandfleet.com/catalog/product.aspx?i=509357&h=080304004&p=1
So far I have not encountered a problem with the roof rack as a possible contender in the leaking Rover problem.
Hope this helps.