I had not heard of The Third Option before, but I looked briefly at their website and I would say it looks like a good program. It differs from Retrouvaille, because that begins with a weekend retreat totally devoted to building communication skills. Then retrouvaille follows up with 6 post sessions. To me, The Third Option looks similar to the post sessions. It certainly would be a great thing for a church to offer. There is surprisingly a lot to be learned about getting along in marriage. And we all just go along muddling through. But the truth is, if you learn the skills, it does work better.
As for your visitation schedule, I would recommend that you work lawyer to lawyer. Your wife is trying to dominate all decisions, and you don't want to rile her. But she will continue to deny you your fair share of time with your kids if you allow it. The boys should be with you on your son's birthday if you have the time off, and she doesn't. Don't let her push you around. It won't make her like you any better.