You are going to have to get the one that feels best to you. Either is a good gun. I kind of like the pistol grips, but that's just my opinion.
The .358 Win will handle just about anything in N. America.
The 3-9 scope is just fine. Just keep it on the lowest setting all the time, except when you might need a little more magnification in a stationary position, like a tree stand, when making a shot at stationary game. If the game is moving, you'll do better on the lower power setting.
The bolt is what cocks the hammer, so yes, it's supposed to hit it.