I think it is important that you tell her exactly what you said here. Do not expect a reply, since what is she to say? But her hearing it will close off one door of suspicion. Like Blackfoot has mentioned, we all have these voices in our head, preying on our darkest fears. If you know of such a fear that she has, address it directly. This will put it to rest as far as what you are responsible for. If she still hears it, then it is now her responsibility, but you have done all you can (assuming you are also consistent in your actions).
“I think if I didn't have this giant uncertainty about the physical side of our relationship hanging over my head, I would have an easier time of making it fun, seeing it as a challenge etc. I'll work on it.”
I do not think there is anything productive in this way of thinking. To me, the only question you need answered is whether she TRULY wants to reconcile or not? If the answer really is NO (assuming you can read into her heart of hearts), then there is little else you can do so go see a divorce lawyer. But I don’t think there are very many people who fall into this category. Therefore the answer is likely to be Yes OR Maybe. The only way to go at this point is with full commitment. Otherwise any hesitancy or second thoughts will be picked up by her and pull you into a self fulfilling prophecy of the NO answer.
In many things, taking an objective viewpoint and interpreting the shades of gray is very important. This is second nature to you since you always try to please. But when someone wants to know whether you care for them, the answer must be an unequivocal black or white. No gray is permitted. That is how healthy jealousy helps to confirm the bond. It affirms the feelings are definitive and she need not have even a twinge of doubt.