Dead or Alive

Question
I am going to group a few together here if you don't mind Sir, I am a first year ump in a league that plays by NFHS rules with a few exceptions, and have some basic Q's to make sure I am calling things correctly.  First, hit by pitch is this an automatic dead ball, or can the runners try to advance at their own peril?  Secondly, in NFHS softball what is the proper call when a batter is hit in the hands while trying to avoid a wild pitch?  I have always been taught that in softball the hands are part of the player, but in baseball they are part of the bat so a hit in the hands in baseball is a foul. Next if a batter is taking warm up swings in the box after the call for the pitch but before the pitcher begins her delivery is this a strike, or something else or nothing,  Lastly a batter settles into the box, the pitch is called for, the batter scoots out until her heels are out of the box, is there a call to make here, when is she out of the box, as soon as she breaks the line or when she is entirely out of the box.  I was told that when the heels break the line any pitch is an automatic strike because the umpire and the pitcher no longer have a reference for the pitch to be measured by.

Answer
Jake,

Hit by pitch is always a dead ball.

Dead ball, take your base.  The hands are not part of the bat.  I don't think the hands are part of the bat in baseball either.

It is only a strike (not talking about a called strike) if the batter is making an offer at a pitch.  Just passing the bat across the plate with no pitch there doesn't constitute a strike.  In you example it is nothing.

The batter must be completely in the box at the start of the pitch.  With the heals out of the box, the batter is not completely in the box.  The pitcher must give the batter time to get set.  If they don't you have a quick pitch, which is a no pitch.  If the batter refuses to get set in the box within 10 seconds of the ball being returned to the pitcher, call a strike on the batter.  If the batter scoots out of the box after they have set and the pitcher throws the ball, make the call based on what happens.  If the pitcher throws a strike call it.  If the pitcher throws a ball or the batter gets a hit, call a no pitch.  The batter or the batters coach should get the idea.