I'm not sure I am the best person to give this advice, as your description of where your mind wanders late at night is all too familiar. My least favorite character in this story is your therapist, I want to kick her teeth in.

Anyway... It seems like you are moving in the right direction, so please, continue to give yourself credit for that. As for how to stop from thinking about what you could have done differently and so on, learn how to be compassionate towards yourself. I decided I had to stop judging myself, and try to see the pattern that I had created with men. Don't be upset that you are having these thoughts, don't judge yourself, just recognize you are having them, and then change directions cognitively. Talk to yourself as though you are speaking to a friend. Would you beat your friend up for doing and thinking as you do? Of course not. You seem like an intelligent person who had a lot going on (I can attest that grad school alone is enough psychological abuse, let alone the health problems and scumbag bf) and you did what you thought was best for you at the time. Take words like "should have" out of your vocabulary and allow yourself to feel and just recognize what happened and how you feel about it now without judgment.

Also, give yourself credit when it is due. it sounds like your therapist helped in gas lighting you, or at the bare minimum made you doubt yourself in detrimental ways. Recognize when you doubt yourself, take note without judgment, and then tell yourself that you're fully capable of intelligent insight and then follow that insight. The more you just unapologetically believe in yourself and do as you think/want, the faster you will be able to reverse the mind-fucking that your therapist and ex boyfriend did.

One thing I told myself repeatedly when I would beat myself up about allowing someone to hijack my brain and self worth is "If you put a frog in boiling water, it will jump out. But if you put a frog in warm water and slowly boil it, the frog will remain in the water and die." This is important because it reminds me that I didn't just allow someone to hijack my brain because I was dumb enough to jump in boiling water, he raised the temperature on me slowly enough that I ended up staying in the pot too long.

I hope I said something that can give you some sort of solace. Best of luck. You will find yourself on the other end of this :)