I think most of us have been a situation that exists somewhere in that grey area between explicit consent and rape. This incident exists in that grey area. Clearly op feels bad about past actions and for now wants to fix his relationship. And it sounds like he has already done a lot to make improvements. (Congrats btw it's not easy to make these big changes)

Unfortunately, I don't think anyone has the answers for you here though. If you want to keep your relationship and work towards a happier partnership you have to talk to your wife. You should tell her how this accusation made you feel. Try to have a narrative around how it hurts you because of how much you care for her. Do your best to not sound accusatory when you say this. And try your best to not get defensive when she explains further why she thinks it was rape. It's going to be another ugly conversation. Just try to take it all in, and do your best not to repeat whichever behaviors she mentions as problematic. Be mindful that it's probably going to take your wife a long time to get over everything. It couldn't hurt to do some small gestures to show her you care too to help along her healing process.

Final thought. A lot of women are thinking through their sexual history trying to identify any experiences we've had that were less than consentual. And as we've done this we identified past experiences that we now view as problematic when we didn't view them that way before. I'm guessing this is what your wife was doing when she said this to you. I'm hoping she was more self-reflecting on her past than accusing you of something terrible. Remember rape exists on a spectrum, and if this is on it it's on the lighter end. And a lot of us are realizing we've been a victim to or a perpetrator of the lighter end of the spectrum.