My response:
I think you're thinking that Divorce, Separation, and Custody are connected. Well, to some degree they are. However, in the latter instance, you don't have to wait until you've been separated for the entire year before issues concerning custody are settled.
If you feel that your separation is imminent, you can file a Petition concerning custody, immediately.
Get yourself a Family Law attorney immediately, and have the Petition papers "ready to go" for filing, and personal service on your wife via phone call to your attorney, the moment your wife tries to leave with the children.
Don't take the law into your own hands - - you let the court decide.
IAAL