I've just been through your thread again (sorry I've not had the chance to visit for a while) and if you have a chance, Go through it again and start noticing all the times when you initiate contact, whether it be to offer help, to call or text her, to give her stuff, to offer to do stuff for her or together, anything that you initiate. The reason I ask you to do that is that it is something I noticed is consistent throughout your thread yet, at the beginning of your sitch your W had expressed that she started feeling comfortable around you only when you started to give her the space she needed.
I know it's difficult and that each sitch is different but IMO, you are still pursuing her too much and this might just drive her away from you. Give her space. If she wants to be with you or talk to you, you live in the same house, she'll find you. GAL. Don't make her your life right now. She doesn't really want to be anyone's life right now.
It also looks like you've got a good list of things to work on so that should be keeping you busy for a while. Give it time. Someone in an older post made the analogy that this was like trying to lure a squirrel to you by holding a nut in your hand. Every time you try to move towards the squirrel, it pulls back and it takes longer for it to trust you again and get closer. Stop moving towards her for a while and see what happens. If she makes the first move towards you, then you can chose to match her move but don't go crazy and scare her away again. Keep a comfortable distance. Match her. If she opens up, listen. If she wants to do something, decide if you want to do it as well. Don't be overly eager to say yes all the time and cancel plans just because she asks. Give her the space she desperately needs right now, and that doesn't mean to stop being cheerful and friendly around her. Just give her space. This is my opinion.
Freshman Class of 2012
M-49 W-42 1D-10 T 10 YEARS M 9 YEARS EA/MLC 07/2010 Separation 28/05/2012 PA confirmed 31/07/12 W Asked for D 31/07/12 D on and off the table since then