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You’ll need the strip caulk in there. Water can come under the windshield moulding and blow in to your box channel. You need to keep water out of there and the best way is to use standard 3-M Strip Caulk.
If water gets on top of the windshield frame it can (and will) eventually rust out the header. It has no where to go if you don’t have any rust in the header and if you do have a hole it will run in the car at the kick panel.
I just bought a box of the 3M Strip-Calk---$13 for 20 yards in 1 foot strips. Doesn't look like enough to fill in the whole header channel though. Looks like I'd have to buy a few more boxes to fill the whole thing in!
Is that what I need to do, or do I just fill in the corners and maybe sandwich a strip of it around the perimeter of the header and the T-top stainless?