Yes the cap goes over everything. You want to trim the seal about 1/16"-1/8" above the pillar. Use lots of soapy water as usual. If need be you can use a razor to pare the tip of the seal so it’s a little smaller and fits easier into the cap. You can use the screw to suck it down but stop if it’s taking a lot of force or it will split the cap. It’s not a bad idea to stick a sliver of rubber into the top of the cap where it has that raised bulge as water can get in that way.
To the extent possible you ideally want the seal flap to cover the edge of the vertical piece. You’ll likely need to use some adhesive and your fancy clamps on the bottom of the hockey stick to get it to sit very flat against the lower trim.
Mine are pop rivets. No idea if that’s original or not. But it already had 1/8" holes so that’s what I had to go back with. If you use them, try and find shallow flat ones so they don’t interfere with the door chrome.
The chrome pieces that I am working with have x2 holes towards the top and x2 at the bottom. Is this correct? The holes are open at the bottom of the body A-pillar, but closed at the top. This is due to body work and paint. Want to make sure that x2 are needed at the top.
Thanks, Bob