As mentioned above, if you are still having a tough time getting the rod free, disconnect the rod on the other side using the pry tool in your tool pouch. Disconnecting the other rod will allow you or a helper to move the top around a bit while you try to get the rod free.
If push comes to shove, remove the whole top assembly and get the rod free. It may sound like a lot of work but it isn't really. Basically three bolts on each side and maybe one or two small phillips screws. With you on one side and a helper on the other, you can lift the top assembly up and off the car.
Also, as mentioned, make sure you check the foam trays for rips. Any small rip will result in water entering the cabin behind the seats.
Here is the DYI link for removing the whole top and frame from Mike Focke's web site.
https://sites.google.com/site/mikefocke2/removingthetopandframe