Why am I so unfit?

Well sitting down playing games all day wont help :P

In my experience of playing Arma, going into prone can speed up the recovery of stamina, no idea why it just seems to work. The stamina in Arma 3 is affected by many things including the terrain, but more crucially the weight of your soldier. Therefore, the heavier you are, the faster your stamina deteriorates. It is also possible you are injured in some capacity.

As for telling your squad to stop, I'm pretty sure there is a command somewhere that will tell them to stop; although don't take my word for it, I don't really do missions or commanding squads.

Edit: I have done some digging on the interwebs and found this which may help you. Also, I asked a friend, and he says if you press Space (which selects your whole squad) you can scroll wheel to Stop to stop your squad.