You know I would never turn down an invite to give advice that will probably involve pursuit. I only know what little you've written, but I like your wife. She's sounds sweet. Reminds me of my own XW.
This e-mail reads to me of someone that wants to talk, touch base, determine whether you are angry, and see if you are okay. She's worried dude. At the very least you need to reassure her that you are okay.
My suggestion is to reply to this note as nicely as it was sent. Address point by point and do not linger on anything overlong. Do not in any way indicate that you are anything other than just peachy (how are you by the way?) and that you are recovering nicely. I would make inquiries about how her trip went, her health, how she is otherwise doing, and thank her for her concern. I would use 2/3 of your reply to put the focus on her and brush over yourself.
I would steer completely clear of anything that even resembles a R talk. And Jak, I know you really feel an overwhelming urge to tell her how much you miss her, but don't do it. And don't end your note with miss you too. It's okay for her as the WA to say "miss you", but as the LBS don't do it.
Jak, something at least made a babystep in the right direction. Since you have been avoiding her, then it might be that. Answer this note, be friendly, confident, strong, and then let her initiate the next time as well. Don't take this moment to ask her to lunch.
In the end, it's not the years in your life that count. It's the life in your years. Abraham Lincoln
It is hard to fail, but it is worse never to have tried to succeed. Theodore Roosevelt