I have a breeding pair. They had a joey who is now 4wks OOP. It is a female. When do I remove dad to keep him from breeding with the joey or mom. Then since I only have one joey should I house it alone when it gets weaned or keep dad alone and leave baby with mom

You don't want to remove dad, he is an important part of raising the joey. When she is 8 to 10 weeks old, she will be ready to be weaned and may leave the family. If you don't want dad breeding mom again, NOW is the time to have him neutered, it's likely that they mated shortly after the joey came OOP and already have more on the way. The best thing to do with your little family (Since no one should have to live alone...) is to go ahead and neuter dad, then they can just stay together. Barring that, you will want to make sure the girl is out of the cage by the time she is 12 weeks when she begins to mature.