Looking good!
I was thinking that a strip of rubber roofing material might work well between the cab and bed.
If you can find really wide packaging tape, that's clear and will zip right over that seam.
Do you miss seeing out the back? I love the visibility out the back in my pickup. I have been experimenting with a "aero-tonneau" lately, and don't like how it limits visibility.
I was thinking about a ridgid, angled cap, that end at a 4" tall vertical piece of plexiglass, instead of even with the top of the tailgate. That would at least let me see if there was a car right behind me or not. Prius' (Prii?) slant down, and then have a little bit of clear at the tail in a similar fashion.
Could you tell us more about the actual construction of your cap? IE "I got out the hair dryer and started melting the material...."