JPSimon,
Welcome back home to the Church! You are responding to God’s Grace in your life and He will help you. Do not discourage.
Before reading my post, as a disclaimer, I am not a cannon lawyer. I am just an ordinary layman. As the previous poster noted, the best thing to do is setup a meeting with a Priest to help you.
Regarding your marriage, as you now know, as a Catholic, you were bound to either marry in the Church or receive permission to marry outside of the Church. Because you married outside of the Church without permission, you need to have your marriage situation corrected before you can receive the sacraments. Therefore, you are correct that you should reframe from receiving the sacraments until you have your situation worked out.
If neither you nor your wife were previously married, it is generally easy to accomplish this. The easiest way is having your marriage co-validated. To do this, you and your wife would simply restate your vows in the Church.
If your wife is unwilling to do this, which seems like the case, there is another potential option known as a radical sanation. Basically, you ask the Bishop retroactively for permission to marry outside of the Church and your previous marriage outside of the Church is then retroactively recognized.
Here is an excellent article on it that the CAF staff did to a question from a woman in a similar situation:
catholic.com/quickquestions/what-can-i-do-about-my-invalid-marriage
As the article notes, it may be possible to go through a radical sanation without your wife’s knowledge in an extreme situation:
There is also the possibility that you may be able to return to the sacraments if you live as “brother and sister” with your wife until your marriage situation is resolved. Basically, you stop conjugal relations until your marriage is corrected. This is, however, something that you need to clear with your Parish Priest.
As for dealing with your wife, when someone becomes religious, it can often make a spouse feel like they are in competition with God. If you show your wife the love of Christ, it will help abundantly. The best thing you can do is love your wife more than you ever have before. I recommend you start meeting your Sunday Mass obligation either at the Saturday vigil or at whatever Sunday Mass is the least intrusive to your home situation. If she won’t let you take your son, go alone until she relents. If she complains about it, say, “Its only for one hour, once a week, and you don’t have to come with me.” Just turn it into something that you do. Overtime, she will adjust.
I’m sure your parish Priest will be able to help you much more. I also highly recommend a Novena to the Virgin Mary Undoer of Knots.
theholyrosary.org/maryundoerknots
I will pray for you.
JMR