Fathers get custody of their children more often than people would have you believe. I would recommend that any father who is seeking custody of his children should make sure that he has everything documented, an also is willing to compromise where necessary. Also, please, make sure that you are not doing so because of some vendetta against your ex. Remember they are her children, too, and do not denigrate your children's mother, especially in front of them, but ever.

The notion that mothers get automatic custody is a going out the window. More and more parents are being awarded joint legal and physical custody. So fathers are now starting on a more level playing field. While it does not always happen it is becoming the new standard. You obviously see that your children deserve better than what they are getting now so it’s time to look at your options.

First you can start with some father’s rights agency’s in your area. Be sure to check them out because some of them are not always on the up and up. Many do great things to help fathers out. They can be a great starting place.
Keep going on your journal document everything. Things will get ugly before it gets better.
When you get to court because the children are older you can request that the court talk to the children and get their views. Let the courts ask the children if they will do it. Not all courts will allow it.

When you get your custody agreement keep it to the letter. IF she is gone as much as you say give her the space to mess up. When she starts putting more and more things in front of her children or does not show up for visitation ect. Keep track and then take her back to court to get it changed. Its not fun and its hard road to hoe but its defiantly worth the fight in the long run.
Above all never speak ill of her in front of your children. Do not discuss the issues with the children. Always be the positive influence with your children. Make sure they know you love them no matter where they lay their head.