First of all I want you to know that you have incredible courage. It's not easy to recognize that your behaviors were causing major problems in your relationship. Many people can't do this and I admire you VERY much for the steps you have taken to improve your marriage. You also went to counseling and have tried to deal with your own issues which is not an easy process. Well done.
It seems to me that at the present there is a lack-of-trust issue that is going both ways. You cannot trust your wife because you know she is prone to drinking, perhaps infidelity and won't take responsibility for her recovery. It's very possible that despite the changes you have made she feels that she cannot trust you. Sometimes a person, BP or not but in BP with paranoia I think it can be worse, can take a while to be convinced that a change is genuine.
I would suggest taking small steps. The story about your mother's day gift to her was beautiful. Do things like that. Connect over your kids. If she needs space or pulls away don't pursue her immediately; she might feel threatened by an action like that. If a time arises when she is in a 'stable' moment; neither manic or depressed, try to sit down with her and ask her if she might be able to define the boundaries she wants you to respect. You can try to take this time to tell her some of the boundaries you would like her to respect as well. I think this is important for a couple who has children even if they split up. Either way there will likely be some long-term relationship between you two because of your children.
Keeping all that in mind, there is a point where you might have to withdraw completely. If she continues with destructive or dangerous behaviors and absolutely refuses to address the issue then there is little you can do. Wellness is a process, it's a struggle and in part it is determined by the dedication of the person seeking it. As wonderfully as you have done trying to change your own behaviors you cannot hand her wellness. You had to earn your changes and she must earn hers.
Above all else, keep a close eye on how she is when she is with your children. You probably already know this but they should not be alone with her if she is in a severe manic or depressive stage. Some people with bipolar can be wonderful mothers, but sometimes the condition can spill out and effect the children. Make sure you explain to them that she is sick, but depending on how old they are you might consider answering any questions they have about her recovery process - or lack thereof - as honestly as possible. If this comes up you need to try to do it in as neutral a way as possible. The point is to be honest to your children without them taking it as a judgement against their mother.
So, in summary, take it very slow. It's a long process and hard on the patience but if it is as important to you as it seems to be it might be worth it in the long run.