Lots of separate issues.
Hindsight is a wonderful thing. She was too young for you to build her a granny flat, she’d have been better off just staying sometimes, and being helped to settle at home. However, you can’t go back in time.
You have a few options, but only you can decide how you want to deal with it.
1: Tell her she has to stop criticising your parenting & undermining you and that if she’s going to be using the house she needs to do her share of cleaning it.
2: Tell her she needs to live entirely in the Granny Flat, and phone/knock etc before coming around as she would if she lived elsewhere.
You have to decide what your boundaries are then make them clear to her.
I can’t see how the additional gas/electric/water are costing you more than the £150 she’s paying paying you pm?
3: Tell her it’s simply not working out and she needs to move out. Tell her she can go and live in the flat her son bought with his £70,000. After all, she wants to be fair, so if his money was ‘no strings’ yours should be too, right?
4: Remortgage, give her the money back & rent the flat out.
5: Sell, give her the money back.
...I’m sure there are other options too.
What you cannot do is ‘do nothing’ when you feel how you feel.