After a couple trips to the dealer, I believe we've got it fixed. The first time I went, they told me that the bars above the doors were both bent (not sure how, but it wasn't something I did since the top's been this way since I got it in March... who knows what the person who owned it before me did to bend 'em). Well, that got me paranoid about warranty since it was caused by something that the previous owner did, but the guys at the dealership (first time I've been to this dealership, and they're my new go-to after the great service I received) said not to worry, that they would fix the bars and everything else needed would still be covered. They straightened out the bars that day, which made the driver's side corner fit tight, but the header was warped so the center and passenger's side still had the gap, so they ordered a new header piece and some hardware to fix that. Took it in today and had everything installed, and they've got the whole thing fitting tight now... looks like it should definitely help keep the water out! And it didn't cost me a dime.