I'm sorry you're here, but happy you found us. There is alot of good insight form so many people who have been dealing with this (in some cases for years). What whe says is probably what she feels...at THAT moment. The next moment may bring something else. She does sound depressed (change of habits to not doing and all the sleep). Is she seeing a C? Is she willing to (if not with you then by herself)?
As far as the chemistry goes, I definately fall into the behaviorist category. If you think and behave as if you're in love with someone (esp. when the chhemistry WAS there) then you start to feel it IMO. Is this MLC? Could be has some ear marks of it. What are you willing to do? Are you willing to love her through this no matter how long it takes with no guarantee of the outcome? What exactly are you willing to do? This is something only you can answer. The right answer is YOUR answer.
I know about limbo (as do we all) and it sux. Do not "wait" for her. GAL and do for you and the kids. This doesn't mean giving up, it means shifting your focus. You can't control anything she does. You can only control yourself and your life.
You mentioned the kids are having problems, is she helping with this? Would counseling help them? Kids will get angry and act out. I'm having an issue with this (D15 and D12). You do the best you know how and you learn more so you can do better.
It's good that you're exercising. Anything to burn off that nervous energy and clear your head. It will help you with your patience too. Patience is the biggest key.