I'm still legally married, but separated from my wife since 2010 in July. Can't get a divorce because we filled for bankruptcy as a couple. Can finalized bankruptcy because the house is in modification. Any ideas?

One thing has nothing to do with the other. You issues of custody with the child you have with your girlfriend is independent of your divorce and has nothing to do with your bankruptcy.

If you want to file for custody and visitation, then go file.

If you're legally married and nothing has been filed in court then you already have joint legal custody of the children. That's not the same as physical custody. If you'd like to formalize visitation or physical custody and you and your wife don't agree then you need to go to court.

I would agrue about not being able to do the bankruptcy but that is another issue and I think you need to re-discuss this since if you are not including the house in the bankruptcy but gong to re-affirm that debt, you merely reaffirm the current debt and still modify it after the bankruptcy.
Of you merely include it in the bankruptcy and just walk away from all of it.

But anyway, yes you can file for custody and visitation. While often done during the divorce, it is in fact separte motions