If you're just cloning for sex, you just want to take the minimum. So, 2 off each would be good, if you are concerned that one of the 2 might not survive. It's good to take the clones from the bottom hormone-wise, but also because those branches are less productive and often get removed anyway.
Those plants look good. I like stocky little afghan/indica's like that. You know there not wasting any height with those tight internode spaces. In terms of your other questions, you can just flower when you're ready and when their about a third of the height you are working with, since they can 2.5 to triple in size. If you are height limited, you can bend 'em. Search under 'LST' . You can top 'em if you want. It just depends on your height limitations. Those look like real short plants though, which is good for you.