I think your W has had an incredible amount of love for you. In all the turmoil from your past she kept on coming back. The sexual relationship following the birth of your children would tell me she was feeling closer and closer to you. That she had put the past hurt in the past.
I think the whole thing with an A probably just made her question who you were and made her doubt herself. Just look at the positive sexual reaction each time the two of you made a child together. Your reaction following that in an effort to "fix" this just made things worse....you probably came off needy and clingy and not the self confident Neil she knew....thus creating more confusion and doubt in her choice.
I will say I am not going to judge you in the above, but I can certainly see how this was extremely hurtful to your W. I suspect she has opted for this sep to give her time and space to heal, for you to do the same thing (my W said a lot of those words leading up to the sep). More important than that she is checking to see who is the real Neil. It is your job to show her the one she married and was attracted to.
As far as good things in your sitch
-I agree D#1 and D#2. This can not be emphasized too much. Look at the effect their birth had on your R with your W and her love for you. They have a huge part in this. Be the best Dad you can be (I know you are great one).
-A very strong attraction and "chemistry" between the two of you. Despite all the things you feel guilty about your W still kept coming back to you....why do ytou think that is.
-A Neil who is finally figuring out who he is and is becoming less self centered and more understanding.....time and patience, show her the real Neil and what she decides she decides
These are the major ones I can think of.
I think and exile from here might help you focus in other areas....we will be here, don't worry.
PS: Just thought I would let you know that my W was out on business last couple days and after reading your "confession" thread last night I couldn't help but think about your sitch all night.....thanks for ruining my sleep last night.....lol....I guess I really care about the people here
TwinDad Me 39, W 36, M 11 W - MLC, WAW???? 2 Kids B/G 3 YRS Old Start of the Long and Bumpy Road..... On the verge of piecing.....a new beginning