Maybe she was molested in her bed and afraid to be alone there? I really think the entire family needs serious family counseling. I also think the youngest needs a more intensive evaluation--not just counseling. Whether or not the investigation can find proof of molestation, BELIEVE the girls and take them for help FOR SEXUAL ABUSE. That can be devestating for the development of these kids. Your wife, as you noted, was a very weak mother and allowed her kids to be in danger. You took on a lot when you married her. I notice you're in the military. So was my hub (for ten years). Sometimes he wanted to do the "miltary thang" at home--rules, you just do them, etc. It didn't work and I stepped in and told them "um, no." With kids you HAVE to be flexible. With kids who've had this sort of background, you're likely going to have problems for years to come, especially if you don't address these issues NOW--and with more than just counselors. You likely need Psychiatrists too. It is hard to get girls to talk about being molested. They feel like it's their fault and many don't admit it for years or forever, but, if it's there, there will be evidence that something terrible is wrong. Your wife sounds young and immature, but you can't help her--you're not trained to help her. I agree she likely suffers from "Battered Wife Syndrome" which zaps women of ALL self-esteem--it is devestating.I've started volunteering at a home for battered women. They come with their kids, crying hysterically, and many say "I made him do it. It's really not his fault." Your wife (or SO) needs her own therapist--perhsps she also suffered sexual abuse as a child and found it to be the norm in her first relationship. All of them need A LOT of help and your life is not going to be a cakewalk. And, sadly, even with the best of your intentions, you won't be able to "fix" them by simple gestures such as bunk beds or being loving. It's just not enough when people have suffered so much damage. You really got yourself into a tough situation, but now that you're there the best thing you can do is get top notch help for everybody and not just chalk it up to "bad behavior." Any sexually abused child or physically abused child is at high risk to act out later in life, use drugs, or get into trouble with the law...or abuse themselves. Please get everyone help, including yourself, just so you can understand them better. This poor little kid whose afraid of her bedroom probably has every reason in the world to be afraid. Somebody probably abused her in some way and her mother did not protect her. I wouldn't force the bedroom issue without going to therapy with the kids and finding out what's really going on, something you can't know yet. Sometimes kids even forget abuse and have flashbacks. I had a friend who was terribly abused as a child and it came back as flashbacks as an adult, which terrified her. Before that, she had constantly been attracted to abusive men. Please be proactive and good luck.
PS--Kids tend to love even abusive parents. That's partly why it's such a sick violation when parents hurt their children (or stepparents).