Did the judge recuse himself from the criminal case? If so, I suggest that you discuss this with your criminal attorney because, even though it's a custody case, the procedure would likely be the same. It's touchy asking a judge to recuse himself. If you lose, you have a possibly unsympathetic ear going forward. If your request is granted, it's pretty reasonable to believe that your new judge knows you asked that the other one be recused and, depending on the personal dynamics between the two judges, the new judge may not be too happy with you either. However, if you prevailed in the criminal case request, asking in the custody case also may be the lesser of two evils. If your criminal attorney won't or can't discuss it with you, then go to an experienced family law attorney in your area for a consultation. The fact that you have criminal charges may have impact on your custody case if you enter a plea or are convicted, depending on the nature of the charges. And, as I'm sure you expect, I have to caution you that going it alone without representation rarely ends as well as it could, even in a so-called normal cases, and yours is obviously not that.
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