As Cadet said...she needs time and space. And judging by her laundry list of items and how long she's been unhappy in the M, it's going to be a LONG time (think many months to years) and a LOT of space (physical S). Start mentally preparing yourself for that now. If your W is anything like mine, your efforts over the past few months only pissed her off more - and one last attempt to show her how much you've changed or trying to reason with her certainly isn't going to help at this point. I think it's time to cooperate with her.
You said something very wise: "my side of the story is a little different...I guess it doesn't matter now".
Bingo. Let it go. You obviously have things to work on. This is the time to retreat and regroup.
There is hope...it's in the letter she wrote you. But you've got to give her the things she is asking for (both directly and indirectly).
BITS M: 35 W: 35 T14, M11 D9, S6 ILYBINILY: June 09 Unofficially Separated (long distance): 1/2/11 W came home: 3/17/11 EE: July 2012 Dropped the rope: Oct 2012 Piecing: April 2013 Not piecing: April 2014 Stuck.