I would put something in writing, email it if you can, so there is a record, and state that he must pay rent from 1st December. You can make it high end of reasonable for your area. You can state that the bills will be shared, or included, up to you. That way he has to decide whether to stay as your lodger or leave. I would also provide a tenancy agreement that states that you live in the house, you are renting him a room only and that you are entitled to give him 30 days notice.
At least that way you will have some money coming in (if he pays) that you can offset against what you owe him for the bathroom and kitchen. Of course, he would have to provide proof that he did buy stuff, did the work, improved it and more specifically that you asked him to. If he just wanted his lodgings to be nicer for his own benefit, then that is nothing to do with you.
From a sensible viewpoint I think it would be fair to pay something towards the costs, perhaps you pay for the materials as he did the labour for free.
He was gaining as well as you by putting a new bathroom and kitchen in, and seeing as he was paying no rent, I think it was fair that he bought and fitted those items in return.
You each paid half the bills, which is fair if you both live there.
But from now on I would formalise it.