I am a stepmom. Raising kids with my husband's ex-wife was THE worst experience in my life. I can only imagine how hard the experience was on the kids (they're in their 20s now.)
My biggest advice to two household families is, unless there is true abuse, to accept and support whatever the other family is doing. My favorite sound bite is, "Just because I am right and we disagree does not mean you are wrong." When your son is grown it will be better for him to say, "My parents raised me in different ways and I really learned about diversity and trust," than "You would not believe how much they fought over flashcards. I don't even remember the flashcards but I remember the nitpick remarks and the bad feelings."
This is his child too (and the stepmom's as well.) They love your son and want what is best for him just as much as you do. And, though I'm sure you find it hurtful, I'll say it again, your son is now the stepmom's son. And be grateful for that. Be grateful she's getting thrown up on with her only response being concern for your son. Be grateful she is concerned about your son's education and general well-being. Stepmoms love children in ways biological moms can't understand. As a biological and adoptive mom I know how much harder it is to raise a child with a non-supportive, jealous biological mother in the background. So, send her a card and some flowers telling her how much you appreciate her and stop worrying about the flashcards. They are so not-important compared to the bigger issues here.
Also, it might help if you address the dad's worries in a supportive way. I like Stormborn's ideas of writing up the things they did. Let your ex- know you hear his concerns and are incorporating them into what you do and that you are supportive of however he chooses to address it himself. You may find that if you support him he is more likely to hear your perspective. More importantly, if you let the stepmom know you hear her concerns and support her actions, you may find that they feel relieved (remember, the stepmom is often the driving force in their parenting team just like legal moms married to legal dads are often the driving force.) Maybe share some of your favorite homeschooling books and articles with the stepmom. Make her your partner, "I've really found this works for me, maybe it'll work for you, too."
Trust me, when your son is in his 20s you will realize (if you haven't before) that the tiny details of HOW you each parented are insignificant compared to the general emotional level and support your son felt. In an ideal family situation flashcards matter, in a divorce situation they are almost irrelevant. It's a hard fact. We raised kids under horrible circumstances. We never got to make a good decision, just "least bad" decisions.
One idea on how you can support your ex's ideas is if it seems that menu items are important to him, you could create menus for your dinners. Hand your son a homemade menu with tonight's dinner written on it. Make a game of deciphering it. Tell your ex and his wife that you've started doing that. They may find it a great idea and do it as well. If they don't, that's ok.
They love your son and want what is best for him. Always remember that.
Created an instant family (7/89 and 5/91) in 1997. Made a baby boy 12/05 adopted a baby girl 8/08. Ask me about tandem adoptive nursing and living as gluten, dairy, and cane sugar free vegetarians. Homeschooling and loving it.