Does the pain of infidelity ever go away?

Two years on, in many ways things are much better. She has tried hard to demonstrate her regret & love for me, and I have done my best to forgive. We are probably more aware of each other and at one level better connected emotionally than we have ever been. I trust her that this won’t happen again.

At the time, someone suggested to me that recovery from this type of event typically takes two years. Yet two years on there is still this part of me that feels a big hole, like a depth of emotional intimacy that we once shared has gone.

Has it really gone forever, or will more time heal it, or is it that I simply have to be more forgiving? Can you really recover fully from infidelity or is it just so damaging that a scar will always remain?

I am so pleased to hear that you and your wife have been able to work through these serious marital issues and are enjoying the fruits of communicated regrets and increased trust.

I like the metaphor you used of comparing this emotional injury to a “scar.”  Scars do not typically (depending on the seriousness of the injury) go away completely.  However, they do fade with time.  And, although when looked at serve as a reminder of pain once felt, they no longer hurt when pressed upon and manipulated.  They become symbols of survival and healing.  They symbolize our inner strength.  Although in some ways I would love to have my pre-scar body and mind back; there is certain wisdom and experience I wouldn’t trade that accompany each one of mine.   

This is the most important sentence, in my opinion, that you wrote:
We are probably more aware of each other and at one level better connected emotionally than we have ever been.
Couples that make it through something as earth shattering as infidelity, usually share similar experiences.  Intimacy takes on new meaning and emotional depths are reached that hadn’t been possible before.  I’m not suggesting that people should seek infidelity on purpose to gain these rewards – but I am saying that there can be some unique benefits to making it through a trial like this one.  Couples that are best able to do this are ones where the one who has been unfaithful shows true remorse and takes the necessary reparation steps, and where the one who has been cheated on is willing to take the time to heal, is willing to forgive, and at some point makes the conscious decision to no longer hold this over the other person’s head.  Another trait of successful couples in this situation is where, although not justifying the infidelity, both are able to take responsibility for possible issues within the marriage.  Affairs usually tend to be a symptom of underlying problems – not the problem itself.  This is not always the case and by saying this I don’t mean to put blame on the spouse who was cheated on for the affair itself.  The choice to be unfaithful is always a personal choice.  I’m just suggesting that there may be dynamics within the marriage that could be improved upon by both people.   
My suggestion for you at this point is to focus on what the atonement truly means to you – and whether or not you want your wife to truly feel the benefits of this gift in her life.  Make a conscious decision to leave this behind – even if you don’t know exactly how to do this.  Look at her through the lens of her choosing you – choosing your marriage – and choosing the difficult yet noble step of repentance.  Allow your heart to beam with pride for her.  
The emotional intimacy you once shared IS gone.  Innocence is not something truly recoverable.  However, a new emotional intimacy – one you are recreating together – is growing in its place.  Enjoy its fruits, knowing the two of you will be better because of it.  There is nothing more powerful than having someone at your side that accepts and loves you in spite of.  
I wish you both the very best.