I'm separated fron my husband and he lives in our house. The mortgage is in my name but he's paying it. Should i wait to get a divorce?

When you file for divorce is a case by case decision.  It depends on how your husband will react.  If he is planning to refinance into his name, only, I gather he is willing to be divorced also.  So, from a legal perspective, there is no reason to wait.  To the contrary, the new mortgage company will likely require an agreement allowing him to receive the property which will enable him to refinance it in his name, only.