LL Rule 6.07

Question
Little League 12 and under.  #3 Runner on 3rd.  #5 batter bats out of turn and gets a base on balls.  #3 runner advances on ball #4 and scores on passed ball.  Appeal to umpire from defense.  #5 Batter/Runner is declared out and #3 runner is sent back to 3rd.  Is this correct?

Answer
CT,

I have a couple questions to ask you to make sure I give you an accurate answer.  If you can give me the batting order as was suppose to be followed, it would help me explain the situation a little bit better.

Also, I need to know what batter was up when #3 scored.

This will help.  Thanks.