Update! This might be your problem as well Stealth. So I replaced my top these past two days with an EZ Top with the upgraded cloth and a glass window. Install went well, first time i have done anything inside the car and it only took me 9 hours. I was considering having someone do it for $400 but decided against it and luckly I did.

So while I was in there I pulled out the drains on either side to find them packed with old leaves and such. I believe this is where my leak was coming from. Looks like the previous owner must have parked the car under a tree a lot or something. So now I have a fresh new top and cleaned drains. The difficulty is I do not know if this would be very easy to do with the top on the car. In order to get these drains out there is one screw facing forward right behind the door and a clip going towards the outside of the car and then you lift it out. I did this with the top off and top frame up so it was easy. Hope this might help.