What should I do about this

That is odd. What do you mean by the school her made her take a breathalyzer? Was she threatened with consequences if she didn't?

Can I get credit for jail time completed in Madison, NY county jail for a warrant issued on CA?

Generally speaking you need to have bail set in a case, wherever that case is, in order to get credit for time.

If the cops are standing right beside the victim without stopping a crime going on (such as mugging, murder, assault), legal?

Yes, police have a duty to assist/intervene if they observe a crime. That is their purpose.

Our daughter was conceived February 2013...is the violation a misdemeanor?

If the Order barred all contact and you two had sex then, yes, there was a violation.

The time limitation on intentional torts like battery is only one year in New York.

Should I pay civil demand or know they won't take me to court?

It would cost more to sue you than to recover what they seek. Feel free to ignore the civil demand.

Is this legal? Do I have grounds to vacate my plea based on this?

That doesn't sound right. Have you spoken to the attorney who represented you in the case?

Will I be able to avoid the misdemeanor record, or should I just plea guilty and pay the fine?

No, you should plea not guilty and fight the case. You may be able to have the case dismissed if this is your first contact with law enforcement.

Does the state of NY have a limited time to extradite me or let me go? if so what is that period of time?

You should have been brought before a judge and provided an attorney already. If you're in jail how do you have access to the Internet?

Can I withdraw my plea and go to trail hoping to get my arson 3rd lowered to arson 4th?

That is difficult to do but not impossible. Usually a judge goes through a specific allocation before accepting a plea of guilty and will not...