Sorry to hear your problems...
You say you are willing to "come clean". I don't understand what you have done wrong, other that to be consummed by daily trials and stress. Who isn't from time to time? Are you leaving something out or am I missing something? Not to imply what someone else here did with indescretions.
I find the comment that she won't go to worship trobuling. Are you of different faiths? Or just different denominations? I should clarify that. Being raised a Southern Baptist, I damn near see Catholicism as a different faith. Has this been a root of your problems? The differnences in churches is the big reason i search faith on my own, I know it can be a divisive issue between people. May God give you both wisdom.
There's a lot of info missing here, not that it's anyone's business, but I think that communication, the lack of, is the issue. I will tell you this, a seperation will NOT solve that. You need a professional third party. If you take this to a minister, please be sure they are educated. I have nothing against ministers without an education, but those with a degree in the mininstry usually have some training in consueling.
Good luck to you, man.