I've been following your sitch from the beginning when you came on the board and now this phase of where you're at. I don't have any advice as I haven't traveled this path. I do feel from your words how hard this is and I am glad you're writing about this so that other LBS's on the board get a sober look on piecing and how incredibly difficult it is. Everyone wants to be in your position without realizing that this process can be downright painful.
I do second LH's red flags. The walkaway/wayward has to go their path and take that time before turning around to the LBS. I'm afraid that she can't handle being alone and she's come back to you, even if she's done everything right by the book as Sandi always talks about.
I don't think your take on her physicality is shallow or superficial. The body can be a reflection of the mind, but not always. It would be hard not to feel that you're getting scraps now when you've seen her at her physical best.
About the men she's slept with, there are just two camps - you can be okay with it, or you can't. There is just no middle ground. I think you have to decide where you fall and that can help in your decision on what you want to do. AS has talked about this a bit and I am paraphrasing in my own words - you can treat her like a new girlfriend and you know that she's had lovers in the past and because you're building something new together, her past comes with her as a package. If you can't do that, then you're better off ending it.