"Instead, I've used black silicon caulk..."
Do not use 100% silicone it is way too glossy
Jim any chance you are near me in PA ?...I would be glad to help
_______________________________________________________________
I have done nearly over two dozen speedster windshields , for the top rubber U channel use electrical tape to hold it in place on the glass, after assembly just pull on the tape and cut with a razor, the excess will retract up under the frame... I always use ALEX Brand latex black caulk from ACE Hardware, it dries flat black and closely matches the rubber and is easy to clean up with a damp cloth.
To bed the windshield to the base aluminum, after dry fitting everything, I run a fairly heavy bead, wait 15 minutes and set the windshield with the base rubber already on the glass into the caulk, I now do the same at the base of the windshield posts too.....( I tape off around the post base with 1/4" green body shop tape)
Snug L & R posts then snug center rod, go back and gently snug the L & R posts again doing this until putting light hand pressure on the center top of the windshield does not cause any upwards movement at the base....As you do this the rubber will close the gap which is usually a bit more on the driver's side cowl area. STOP you're done that's all you need to tighten it.