just an Ideal
the ttop seals you have you say dont meet each other or are not meeting the glass?
if they dont meet each other, did you keep old seal if so cut piece 1/4 to 3/8 longer than space put silicone 100% clear on bottom and and w/s adhesive on side put in place compressing patch in place take duct tape and tape down add small amount of wt to secure to roof. let dry should hold and seal.
If weatherstripping is'nt touching glass, get a 500 cc syring with large bore needle put 100% silicone in it inject a small amount in several place about 1/2 apart along area starting before and ending after gap .
insert needle into middle of w/s rubber closer to roof line than top of rubber, a small amount all along the area this will cause rubber to swell. place ttop in place do not lock down only looking to see if space is closing up let dry
if injected right will swell rubber up toward ttops will harden inside but will still be soft seal on glass
just a couple Ideals