Kyle, bear with me on this one.
Your story touched on a lot of memories from a long time ago. Except that when it happened to me, I was the friend who slept with my best friend's wife.
Here are a few things that might give you some comfort when you're feeling angry:
1. If your wife cheated on you, she'll probably cheat on him. It's a character flaw, not a once-in-a-lifetime event.
2. When (not if) that happens, he'll probably feel as bad as you do now (Karma works that way - I know it did when she did it to me).
and most importantly of all
3. Go and find a lawyer today, if you haven't already. File first. And fight as hard as you can for FULL CUSTODY of your son!
Right now, your wife is living out of wedlock in the heart of Mormon Country. I don't know Utah, but I'd bet money that with a sympathetic judge you could force a VERY favorable decision because of this. Things aren't like they used to be where the mother automatically won. I know because I took custody away from my ex-wife three years ago. It can be done.
If you wait and let her file, her lawyer will do his best to screw you to the wall. He'll do it because (no matter what agreements the two of you may make beforehand) by screwing you, it provokes a prolonged fight. Prolonged fights put money in his pocket (and takes it out of yours). If your wife said that she considers it all to be your fault, she will see nothing wrong in fighting dirty to win. Therefore . . .
Keep a journal of everything; every conversation, every slip of the tongue, every questionable thing that might be the one thing you need to win. Get your ducks in a row before going into battle.
Remember, your son needs someone like you a lot more than he needs someone like her. Don't let him down.
Lastly, if you win custody, your wife will probably try to reconcile with you. If she does, a premarital agreement guaranteeing you full custody should be the first thing you think of.
"Fool me once, shame on you. Fool me twice, shame on me."