Hi OP,
I thought I'd comment as a couple of years my DM and I bought a house together. I live with DP and my DC and she lives with my stepdad.
Before we bought the house we had to have some very honest conversations about what would work and what we all wanted. There have been rows along the way but it's settled down into a workable solution.
We created an annexe that is entirely self-contained for my DM and stepdad. We are lucky as we're on a corner plot so they have the side garden and we have the back garden.
For us, there HAD to be a degree of separation - we had to share a kitchen for a while when we were doing the building work and honestly it was hell.
As many PP have said, you need to sit down together and just say this isn't working in the current format. No one is happy - she's annoyed at you mentioning manky rotten fruit and she's niggling at you about leaving the dog food out, let alone the issues with not being able to switch off and relax in peace without the need for conversation.
I think you need to say that changes need to be made and that you can decide on the right options together. Tell her the options are that either you sell up and go your separate ways - and she gets her 10% back minus her share of any fees - or you find a way to create independent areas within the house without the need to share facilities.
I would say that even if you have to borrow more to do some building work, it would be worth it for the peace of mind you'll get (assuming that you can afford it). I've got a thread up somewhere about the building work we did.
Even if she was the loveliest soul in the world - and it doesn't sound as if she is - then sharing spaces is pretty difficult. We have an internal connecting door between us and DM - we've had to train her to knock which she wasn't best pleased about. The other thing we do sometimes is prop our washing airer up behind it so that she can't come bursting in, even if she wanted to.
I would really urge you to try and make some changes - this isn't something you can just live with.
I'm happy to answer any questions about our set-up if it helps.