He was making me do things over skype
In what fashion was he "making" you do anything? Disconnecting a Skype call is not a complicated thing.

he found them and was threatening to send them to the Indiana School Board.
And thinks the school board will do...what?

My parents are divorced, would one try to fight for custody from the other,
We don't know your parents and cannot predict what they will or won't do.

and would I be labeled as a sex offender?
Possibly. I'm sure you've heard of the girl here in Ohio who sent naked pics to her friends and was brought up on felony child porn charges. In Ohio, judges have discretion as to whether to order a minor to register. In her case, she did not have to.

And my third is what would happen to him
He could be charged with possession of child porn. Probably corruption of a minor. Possibly online solicitation of a minor for sexual purposes.

and would the court favor my case?
We can't make any predictions.

What needs to happen now is that you need to tell your parents EVERYTHING.