He doesn't want the money back, he gave the same to SIL when she bought her house a few years later, it was a gift.
If you won't speak to SiL, & DH won't speak to FiL, you are either going to have to accept that your home is never truly your own & suck up the contanst intrusion ... or Use Your Words.
Nobody can do this for you OP.
A gentle conversation is all it will take. Getting the first words out is always the hardest bit, but from there at least you are actually COMMUNICATING.
You could try many different approaches - generally it's best to soften 'bad news' by getting 'good news' in first - FiL may have made a pest of himself, but he's just one human, it seems oblivious to the angst he is causing you.
"FiL you know I like to make you welcome here, you are such a big part of our family.
But I found it a bit weird you brought your friend round without giving us notice of it, & then didn't feel it was worth mentioning for 3 months. I know you are family, & I'm glad you feel comfortable here - but most people would feel a bit odd about a stranger in their home without their knowledge.
Also ... & I'm sorry to even need to say this - my NDN has just mentioned that you are always round here while we are at work. I don't understand why you feel you need to be here without us here? So - embarrassing as this may be for both of us! - I am asking you not to come round when we are not here unless there is an emergency.
I'm so sorry but while we're getting this out of the way, there's one more thing. Sometimes DH & I want to lie in or just have time with the kids on a weekend. So instead of you just coming round every weekend at 9am, could we start making proper arrangements to see you? As the kids are getting older we are all going to be busier, & I want to make sure we still have proper family time with you.
How about we visit you for a change this Saturday afternoon, & you come to us at noon on Sunday for a big family lunch?"
Obviously you are going to get some pushback, maybe some spluttering, maybe some hurt feelings or even outrage.
But press on - get it all out in the open & at least then, no matter how embarrassing it all is, you will understand what his take is on why he feels so entitled to your private space.
With that understanding, you can start to negotiate. Without it, you are stuck forever in a situation that is making you miserable.