that "wire" will come out when the top is put down so if you pop it back in with the top up, it will most likely not seat correctly when putting it down/up the next time. Like I said, it's a common issue with both sides. I have just lived with it as it doesn't really impact the tops ability to close or properly seal.

Well I hope there is a way to adjust it. I had the top up on the way to work and it definitely has an air leak sound on the hi-way. Even if it doesn't leak water, I wouldn't want to listen to it on a long road trip. Screwing the end of the cable into the frame helped close the gap, but I hope to somehow close it more.

On my 2001 there was thsi same issue when I purchased the car. YouTube has several videos how to fix this issue.
I do recommend fixing it due to air/water leak issues at least of hiway speeds.
Also if the cable stays outside the metal 'bow' for a while s(weeks etc), it will make scratch marks that you can fix only by painting the 'bows' again.

Well in addition to the cables not wanting to seat correctly I discovered a different problem. The back of the windows don't seem to seal to the weather stripping on the top. It looks to be the same on both sides, I think that is where the wind noise is coming from actually. There is not a big gap but it doesn't look like the windows are touching the weather stripping or if they are it's just barely. The stripping looks fine on both sides so i'm not really sure what the problem could be.

So the top of the window seats properly but there is a gap along the rear edge of the window? That's bizarre.

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Yes it's almost like the frame isn't wide enough. It almost seems like I need to put a spacer between the inside of the frame and the body before I bolt it up again. Looking at my other car it seems like the frame sits closer to the outside body panel. I'll take pics of the two sometime this weekend and post them to see what you guys think.