39 AF points in Nikon D5200. Can I manually focus each one of them? - 1

This is one of the things which is making me to go for D5200 (rather than D5100), If I can't manually control all those focus points, I would rather go for D5100

This video explains the Nikon AF system really well. Skip to 1:30 into the video to see the AF points explained.

You're not getting it right. Those are AF points, meant for the camera's computer. Since you're better (ideally) than the camera (and it's computer), (hopefully) you should be able to focus anywhere on the viewfinder using the ground glass focus screen.

From experience though, I find it best to focus manually at dead center before reframing and taking the shot.

You can manually or use auto-focus using any of those points

They are there so you can focus your subject when it is NOT in the middle of your composition.

This means you can focus and will not have to recompose the shot.

How much experience do you have using a fully adjustable camera?

My camera has 51 focus points and over the course of a year, I use every one of them, usually when auto-focusing my subjects. Those points are especially important when shooting sports and action when using continuous focus and following the subject across the playing field

When you use one of the focus points and manually focus your lens, you will need to use the electronic rangefinder. It will key on the point you choose