There are presumptions in regards to parentage that might come into play here, so the state police probably aren't going to charge him with kidnapping for taking the youngest child. By and large, state police are powerless to act in family law matters, which are outside of their jurisdiction.
My suggestion is to try your best to co-parent, even if he refuses to do so. The court is, with growing frequency, making its final orders on what is sometimes referred to as the 'friendly parent' doctrine, whereby children are placed in the care of the parent most likely to support and encourage the children to have a meaningful relationship with the other parent. Thus, if you're the 'friendly parent', your chances of an outcome in your favour are significantly higher. If you're the hostile parent, those chances reduce dramatically.
I assume you have sought legal advice in relation to the initiating application, as well.