Batter Steps on Plate During Swing

 
With a runner on second base (R2), the hit-and-run is on. The pitch to the left handed batter (B1) is well outside the strike zone, so B1 steps on home plate, swings at the pitch and misses it. The catcher's throw to 3rd base is late and R2 is safe at 3rd base.
 
The defensive coach thinks the batter should be called out and R2 returned to 2nd base since B1 stepped on the plate. What does the umpire do now?
 
Extra Credit: Does the call change, if in the situation above, B1 stepped on the plate and then foul tipped the pitch. The catcher caught the tip and then successfully threw out R2 at 3rd base?
 
Call
In NF, when a batter hits a pitch while his foot is touching home plate, the ball is immediately dead and the batter is out (NF 7-3-2 and 5-1-1b). Any runners must return to their bases at the time of the pitch.
 
In the first play below, although B1 had his foot on home plate, he never contacted the pitch -- so there is no penalty and play on. In the extra credit question, B1 did contact the pitch while his foot was on the plate, so B1 is out, the ball is dead, and R2 returns to 2nd base.