Where do we start!?

[pearlharbr]

Sounds to me like you need to either go to marriage counseling or seek out a plan to follow.

I understand being scared that she will walk out again, I'm dealing with that myself. But the only thing that will fix that is time. If you deal with your other issues and establish good communication practices then both of you will feel comfortable discussing issues before they become so big that someone feels the need to leave. Or if she does want to leave again you can discuss it and it won't come as a total shock.

Currently my BF and I are working through the exercises in "After the Affair" with the understanding that if I don't feel enough progress is being made we will start seeing a couple's counselor.

FWIW, I insisted on total transparency/no contact before I would even discuss working things out. Perhaps the affair was the result of underlying problems but that breach of trust and disrespectful behavior was so huge that, for me, it must be addressed first before getting to what caused it.