I noticed a pool of water just under the back window. Looking at the outside of the top it looks like there is a channel between the canvas and the bottom of the glass were it looks stitched. Should this be like this or is it supposed to be attached I will try and attached a photo in the morning

 

Here is the photo

 

Yours is in a lot better shape than mine is. Yes, they come attached, but over time they pull away. In some post or another around here some years back, somebody gave a fix for it (I believe some 3M or other brand adhesive).
Also you might want to check out this thread:
https://mustangforums.com/forum/conv...tang-vert.html