The first mistake you made was agreeing to having one spouse be a stay at home parent. I lived this and it often leads to resentment in a relationship. It can work but rarely does. If your post is real I see some real red flags in your behavior. First, you state you have afforded your wife the opportunity to be a "stay at home mother". I can't help but read the attitude with the quotation marks. I'm sure at some point you probably both agreed to this for whatever reason but clearly your expectation and her expectation of being a stay at home parent weren't matching up. Then again she isn't really just a stay at home mother because she started her own business as an "artist". Again with the quotation marks as if an artist isn't really a job. So she takes care of two young children and is making $25,000 a year as an artist, which is hard to make even as a full time artist.
A year ago you realized the marriage was in trouble so you turned to running again, which has been a great thing for you to cope with the marriage falling apart. But what about your wife? She sees that you can come up with time for running but you can't manage to watch a romantic comedy or musical because that isn't your thing.
As far as the money because that seems to be your main resentment. Why is everything in your name? I've seen this before and often is a control mechanism or perhaps you feared some day she may leave you so you wanted to stack the deck against her. Where is the money she makes going? Does she stop at the market and pick stuff up for dinner? Does she buy things for the kids? If she does than that is part of household expenses. Perhaps she is stashed some of that money away because she could see the writing on the wall. Her name isn't on the house or the cars so I can't say that I blame her.
Staying at home is glorified by those who don't do it. It can be a lonely and isolating experience and the working parent just thinks it is all fun and games while they are working all day. There were days when I would have loved to be able to go to work for the day or even spend some time alone in the car driving to work. Your wife started her own business while managing two young children and that is not easy. Maybe she would be making much more than $25,000 if she didn't have the childcare responsibility as well. You married young but she was even younger. When did she have the time to be on her own.
Did you ever discuss moving together as a family to where she is from? After all she has spent the last 6 years there while you focused on your career. If you had the support system of her family you would be able to get out together and work on your relationship.
In a later post you stated that you helped cook and clean and you put the kids to bed every night. Why shouldn't you? She works too. So she takes care of the kids has her own business and she is supposed to do everything around the house too. She is supposed to be an equal partner not an indentured servant. As far as putting the kids to bed at night that is the best parenting job there is. My husband would read the stories to the kids, tuck them in and get all the love and attention from them. Try getting them up in the morning when they don't want to get up or are pitching a fit because their sock isn't in the right place or the only thing they will wear is shorts and it is snowing outside. Not to mention they are your kids too.
Maybe you can still make the marriage work but if you can't I really do hope you are a good saver because your 401 certainly doesn't indicate that you are. You will definitely need that money to hire a good lawyer because there is no way she is going to take the shitty offer you have made to her. The harsh reality is that no court or judge is going to side with you with you like the majority of people on this message board.