My fix, literally was I had to order a Limited with no Sun Roof.
I did the same thing.
I could have had my Jeep a week earlier with over a 100 fewer miles on it had I been willing to get one with a sunroof.
Instead, I wanted one without and the closest match came from Boston as opposed to elsewhere within Connecticut, but far closer.
I had a sunroof on my first used car. It was a factory one that actually slid inside the roof behind it, rather than on top or simply popping up. While I never had any problems with leaks, I hardly used it. I tended to only open it when went out to the car on a hot day so I could vent the heat quickly out the roof.
The thing I did run into, though, was a clog in the trough that runs between the windshield and the hood.
One day during a hard rain, I found the carpet was soaked. I thought it was the sunroof, but everything was dry. Checking the floor, I didn't find any leaks. That's when I realized those little "helicopter" seed pods from our maple tree had plugged up the drain holes in the trough and the water was overflowing through the dash.
So, while I realize this isn't everyone's problem in the thread, it's something everyone should watch out for. Even with the screen they put behind the vents, small stuff can lead to a big clog later.
It's easy to neglect that trough when you're washing and waxing your baby...