Hi Houston,
Welcome to SR!
As a recovering alcoholic wife and mother, I can tell you that you should go with your gut instincts. I can not believe the number of times that I lied straight to my husband's face about my drinking. I did things that I can not imagine doing today. One time I ran out at 10 at night to get more wine (hubby worked graveyards then) and my daughter was asleep. She was 7 at the time. When I came home 20 minutes later and got out of the car, my neighbor from across the street yelled for me. I turned around and there was my little girl with dried tears on her face from waking up and finding herself alone. She went to the neighbors (smart girl). The next day I told my husband the story but told him I ran out to get tampons. Ugh. Anyway, the point is, she is drinking no matter what she tells you. You could always buy a home breathalizer while you are figuring this situation out with the separation.
Okay I will now leave it to the "professionals"
I wish you the very best of luck with your very difficult situation.