for that application, I recommend SIKA MORTAR FIX, available at home depot. I discovered it last week, it's a lot more fun than any other plastic gap filler, except SIKAflex self-leveling sealant. At first I tried using self-leveling sealant for vertical gaps, but it just left a thin coating and the remainder dripped down the wall. Fortunately, the Mortar Fix and self leveling sealant appear compatible. I successfully plugged gaps over 1/2" wide with the mortar fix.
You will need to stuff something into that gap, or you will empty a tube every 4ft. Like you were saying, don't use "Great Stuff" unless you have complete confidence in your technique. Removing excess foam is a waste of time, and if it touches the glass, you will have to start over.
You can touch it up with your finger but you might want to wear plastic gloves, it is very tacky. If you get it on your skin, you will need petroleum solvents to get it off, but you can wipe it off to the last 3%. If you apply to much to the workpiece, you better not waste your time trying to remove it; Just trowel it thin as possible then paint.
Neat properties of SIKA products:
paintable
trowelable (especially "mix-n-go," it comes with a free trowel)
the mortar fix looks like real mortar
cross-compatible?
adheres well to masonry, but can you plaster over the SIKA?
I have results to show for, I'll take a picture tomorrow.
Finally, try the mix-n-go, it costs less than half as much and should be the same plastic. I haven't yet, I'm waiting for an ideal application.
Now, if you could tell how to tighten up the Staff bead and other seals... and my windows rattle a full 1/8"!!!!!