6.75 inches from the top of the mounting surface of the rod holder
Yes they are angled, probably less than 30 degrees, and yes they do have caps.
My recommendation for installing the rod holders would be behind where you sit in the kayak. Reason for this is when you are paddling you will not bump your fishing poles and they will be behind and out of your way.
I think mine just came with screws for securing into wood (pontoon deck, dock, etc). If you want to mount in aluminum or fiberglass, you are going to have to get your own fasteners. I might have even bought my own stainless screws come to think of it. I'd contact seller if fasteners were in description?