I have to tell you...your relationship with your wife has me stumped!!! By all appearances you have a good relationship, you work well as a team. I believe based on your posts that she loves you at some level at least. When she needs emotional support she turns to you. You both are great parents.
What is missing??? What is the allure of her living apart? Its not like she is running the bars etc? Yeah she has Tom in the background...but when does she have time for him?? She seems consumed with work and then the kids....with little or no time for much else. Financially this is a disaster. The kids have been forced to go back and forth instead of having a single family structure.
I get the situations where people fall out of love for people. The old "I love you but and not in love with you" BS. But all long-term marriages go thru that at times.