I read through some of the resposne first and agree with most that the mother is threatened by you and as a step-mom you have to take a back seat in this.
I have been a stepmom for 6 years now. and for the first 3 yrs. My stepdaughter lived with her mother. When I came into the picture, my husband was refused almost all of his visitation, she wasn't allowed to go to our wedding and my husband went a 7 month period before he was able to see his daughter because the mother was so threatened by me and my potential relationship. phone calls were never returned and we had to eventually go to court to resolve the matter.
My stepdaughter has lived with us primarily for the past 3 yrs, with little to no visitation with her mother.
So here is what I would suggest:
1. Be in the same page as your husband, if you and your husband are disagreeing on issues with his ex and his son, that is not good at all. It will only cause problems between your relationship with your husabnd and you will become resentful. I went through this phase in the beginning of our marriage. He would listen to everything his ex would say and then he would come to me and start in on me about how he was hurting is daughter by being with me and it was tearing him apart because he wanted his daughter to be happy, etc. After visitaitons, his ex would call and say that his daughter felt left out and like she wasn't apart of our new family, etc. and I would look at him and say "open your eyes", you just had visitation with your daughter and did she act like a child who was being left out. Eventually he got the picture...
2. Stay out of it... As much as you want to help, you cannot. You can only help your realtionship with your husabnd by creating a united front and let your stepson know that you're there if he needs you. I became heavily involved from the beginning thinking I could do more for my stepdaughter and give her a better life. Yes, I know that I give her a better life and do more for her than her mother ever did, but the fact is that that is her mother and her mother will always be #1. NO MATTER WHAT THEY DO. And in order to save my sanity, keep myslef happy and not continue to get hurt, I let my husband handle everything.
3. Let your husband deal with all discpline issues with son and ex-wife issues. Like I said before I became heavily involved in the begginning thinking that by me intervening that I was helping and it was not. Mother became only more threatened by me and stepdaughter eventually started to resent some of the things I was doing. She alwyas wanted to know why I spent more time with her and did school functions and her mother never did and why can't her mother be more like me and she evenutally started acting out towards me and blaming me for her problems with her mother. And then whenever her mother we do 1 little thing it was all she would talk about for weeks on end and my feelings would be so hurt because here I was raising her and caring for her, getting her to do better in school taking her to tutoring, meeting with teachers and she gave me nothing but attitude. So I have learned to step out of picture a lot and let me husband handle it.
4. My stepdaughter does counseling every two weeks, my husband is taking a parenting class on how to raise troubled child because that is what we are dealing with now. For you, I would reccommend counseling for your stepson, a parenting class for you and your husband on blended families and co-parenting, if your husband can rally the ex to take the class the better. You can find these classes through the community, usually like a Family Stress Center type facility, also when you go to Court over custody/visitation issues it looks better on your end if you and your husband are in a parenting class and usually the mediator at court can provide a reference. Check with your doctor, I know Kaiser has the resources for these classes as well.
5. Back to on the same page as husband, If an issue arises with the ex or my stepdaughter, my husband always confers with me first before he makes a decision, so I am not totally out of the picture where I have no say in anything, I do. But everyone else just doesn't know it because he is the one who addresses this issue with him NOT me.
Best of Luck! And realize that your stepson is going through a lot and school will suffer as a result of the emtional instability he is being put through right now. The best thing for you to do, is let him know that you are there for him if he needs it, if dad can spend "one-on-one" time with him the better and if dad can rearrange his work schedule to accomodate picking him up from the afterschool program the better, mom will be less threatened by dad.
And yes, eventually the mom will get over it. It took my husband ex 6 yrs. and counting, she is getting better, but it took her losing her daughter in a custody battle to open her eyes and begin to understand that what she was doing was not helping, but she still has her moments.
All the best!