Thanks for this thread! I've had a series of similar leaks.
At first, I thought it was just a crack in the fiberglass mid-top that I found at the back center above the center brake light on the high top. I fixed that with fiberglass mat and that helped.
Later, I put a bead of Proflex sealant around the top part of the black trim around the top. That helped, but like shadetree said, it was just a band-aid.
I have a 1990 E350 EB. I didn't realize how poor the gutter system is. During heavy rains, the water pools up in the gutters and I believe it's entering in the screw holes as well. So, I'll be doing a similar repair soon. Taking off the trim, replacing screws with sealant, etc.
1990 Ford E-350 EB - Home Build in Progress - 121K