Wow James, you seriously have had some heartache to deal with and I really feel for you mate. I would say the sequence of your events in your current ex losing her feeling for you is very similar to mine, although my ex refuses to acknowledge there is a problem and that I am essentially the cause of her anxiety and feeling down.
I have done a lot of self reflection today, chatting to my parents and I am starting to realise that things were not right, some of the things I liked about the relationship were a bit shallow and material which is not healthy but there is also the emotional connection I had with her. This is what I find hard to detach from. Whether it be family issues, her Mother's death, work problems she would confide in me and almost make me go through the issue with her so I feel we had this deep connection that I hadn't had in previous relationships.
I have sent the email apologising for my behaviour recently and tried to reset the balance after coming across as needy, so hopefully if I leave her be the negative feeling towards me may subside and she will remember the positive aspects of the relationship. My only fear is that before I pressured her I had said after our final meeting on Thursday last week that I would leave her be for a few weeks in the hope we could catch up and reconcile. This morning after pressuring her she texted me with a message she had already typed up basically saying that she didn't need to wait a few weeks as ultimately her mind is set that this isn't right and she doesn't want to hurt me or stop me moving on faster, She said that whilst we had some special moments that she will cherish, we are not right for each other and that's it. It all seemed very final, very structured and certainly wasn't written in haste so I really don't know what hope I have.
I guess the one thing she hasn't been able to do yet is miss me, miss the things we used to do together and maybe it will take going on a date with someone else to realise that. I just hope that is a possible outcome still if I leave her well alone for now.
One of my biggest issues is I'm not used to being alone and am not particularly good at it, so I tend to try and fix things and if I can;t fix it look for a replacement. I know I need to hold out this time until I know she's either moved on or really isn't going to change her mind.