I totally understand where you are coming from. I happen to live in the heart of the largest Amish community west of the Mississippi in the US and I have Mennonite family on my mother's side.
Can you go back to the court reporter and both the attys. and ask them if they would make statements to what they told you? Now, there's a very good possibility that they won't, if this judge has a strangle hold on the legal community there, no one would dare go against him if they still have to continue to work with him.
But the ONLY way you 'might' get some relief on this is to file an appeal. If the court reporter and the attys. refuse to help you willingly, you can have them subpoenaed...basically an order telling them they have to appear to testify. But if this judge's religious bias is that well known, he has no business presiding in a court in that area. Which means he needs to be reported to the state bar assoc. and the state atty. general's office.
Recently, there was a custody case near here involving an Amish woman and 'English' man (she had a baby out of wedlock, if you can believe it and if you know Amish, you know what 'English' means). The father asked for joint legal and visitation and the mother wanted to cut the father completely out. The court ruled in favor of the father.
You have an uphill battle against you. There's no question about that. And it will cost you plenty. Talk to your atty. and see if you can get the ball rolling on an appeal. I know of an atty. here in my area who comes to mind who has done high profile cases, but I don't know if they have any contacts in your area. And feel free to send me a personal message through this website if you want to discuss this privately. Just click on my name and go the the e-mail link. I may not answer immediately (it's my home e-mail and I'm currently at work) but I will answer as quickly as I can.