Here is my situation and short as I can make it. My Gf had problems where I was not giving enough attention at times but there was still a lot of love between us. She got in to a friendship with another guy who used to beg her to leave me and give him a chance which she said she would never do. Our relationship problems began fix and thing began to get better but the guy was still around which I told her I had a problem with and unknowing to me she began to slowly distance herself from him.
Then she lied to me about and incident concerning him and I broke up with her because of it. She was really hurt so she stopped all contact with the guy and was begging me to come back. I eventually did go back but the I really was not ready because I didn't fully let go of the issue we broke up for and the caused a lot of problems in the relationship and things were worst than they had ever been. We separated again and I did a lot of introspections and only then did I realise a lot of the mistakes I made in the past that I mentioned above. We eventually decided to have a conversation to bring closure but it turned out after all was said that we would try again. The only problem is that for the period when we were not in contact she made contact with the guy and they got really really close.
Since we got back and with the personal changes I experienced from my period of introspection she told me I'm all the things she wanted and more and she could not ask more of me but she just can't get the other guy out of her system. I ask what she wants and she tells me that she strongly believe that a relationship with the guy is wrong and that she still love me but its difficult to get him out of her system.
Since we got back the has been improvements as we would have good week when she misses me and calls be up we try to do a lot of stuff together and we have a lot of fun with each other. Then the next week she would begin to wonder how things might have been with the other guy. He used be call and beg her to come back and she said not, she eventually told him to stop calling or texting her phone.
We are still together and every time things are going good I forget we have a problem and she even made a joke and asked me when will I marry her and she would not have done so if she was not really feeling for me. The she slips back into the moments of thinking about the guy and it hurts me because she can no longer be affectionate and passionate with me.
She called me yesterday and told me she is going to stay away from the both of us and spend some alone doing some introspection and make a decision but I can still call and she would still call me just to see how each other is going.
I would like to know what's the best thing to do to increase my chances of working out things between us and she getting over the guy.

Just my opinion, but I would leave her alone, and let her make up her own mind. Others may disagree, but a female with confused feelings can go either way. You have a history and have forged a relationship, and should not have to play games, or jump through hoops to prove yourself.