If you are that concerned ask him not to spend so much time with her and especially in her bedroom with the door closed but you must keep a very close eye on that behavior you don't want to wait until it's possibly too late and something does happen, I don't think your daughter knows any better and just thinks that he is spending time with her but maybe talk to her and see if he ever does anything inappropriate while the door is shut it is strange for him to spend so much time with her and if it is so innocent then why must the door be shut? Also him doing her homework for her is crippling her learning and enabling her to be lazy because her step father does it for her, tell him to no longer do her homework and make her more responsible to do it herself. You need to make it very clear to him that this bothers you and you have reached the end of your rope with this situation.
His actions are troubling because he may have lost touch with the reality that he is her father figure though nothing may be happening he isn't understanding that this behavior is not the normal, no father or step father spends so much time in their daughters room and with the door shut, next time you see that they are in the room and the door is shut call your husband out and tell him you no longer want the door shut and he needs to stay out of her room. If he doesn't respect your wishes as her mother then you may need to give him an ultimatum either get help with this behavior or you may have to take more drastic measures it is more important for you to ensure your daughters safety than to make your husband happy or ignore what is happening and it's good that you are noticing this because so many mother don't realize what is going on until it is too late and the physical and psychological damage has been done.
It would not hurt to check in to some counseling both individual for your husband and family counseling just to make sure that nothing has happened to your daughter and the counselor may be able to get your husband to realize that his actions are inappropriate with a teenage daughter.
So what you are saying is that you really don't have any say as to what he does with his daughter? He may just want to make sure she is okay because of everything that has changed in her life, the divorce, marrying you and have a new baby, she has been so use to having all of his attention but still their relationship seems a little more strange than most father/daughter relationships and it must be addressed and if you feel that he isn't listening maybe being honest about you thinking about leaving will get him to listen. Only you know how much you are willing to take and when you've had enough but I think counseling for the family would be a good idea and possibly a last resort on your part.