Ok I have a little more food for thought for you people. (after all those wonderful answers)

My S was vandelized about 5 months ago and I had the top replaced at a local shop. Asthetically, the top looks great. I am therorizing here, but what I am thinking is that somehow they could have possibly blocked the rain drains, and now it's coming into the car?? I'm going over to the shop today to talk with them about it.

I wasn't looking for a lot of people to state the obvious like throw a tarp over it, but instead I looking for someone who has maybe had a similar occurence and can provide some insight.

If any of you are "fortunate" enough to have your S vandelized and your seats stolen, then maybe you won't be so quick to be smart.

 

The rain drains are build into the rubber seals. I don't think you can mess those up unless they're warped. The most common point where it would leak is the seam for the seal halfway across the top of the window. I would look into getting some shin etsu grease and treating the seals (especially where they join with other seals). That might solve your problem.

 

I just went to the shop during my lunch break and they told me that most likely, they disconnected one of the tubes that connect the drainage system to the wheelwells. They're going to take care of it and make sure that it doesn't leak anymore.