The mopping up was actually anticlimactic. After all the time they had spent worrying about it, Hermione was able to make the adjustments needed to prod at the magic outside the estate wards on the first try. With that kind of access it was almost trivial to rewrite the nature of magic in that world. When Harry finally went to the portal and teleported out to decide how they should proceed it was like taking candy from a baby to track down all of the Voldemort revenants and destroy them. Hermione remained in trance throughout the process to maintain her patch every time Merlin's interdiction runes tried to correct her changes, but from Harry's perspective it was a cakewalk.
Finding any sort of viable remnant of magical Britain's public infrastructure proved harder as he explained to Hermione at length. "The institutions that you remember existing are now Voldemort's through and through. I can't find a single wizard alive who I would trust to sell me a wand much less run a government."
Eventually Hermione decided that what might be best for her world would be to remove magic from it forever. I shall be sad to see it go, but it has brought little happiness and much chaos to our pitiful world. I think that we may be better off without it.
And so Hermione herself wrote the new endcap that she placed on her world's structure. Removing all of the runes from Merlin's all the way back through the hack that allowed magic to work in the first place, Hermione fixed the one flaw in the core runes, and added one new rune of her own that would obliviate anyone who ever started the singing chant of the runes.
Even returning home ended up being easier than Harry had expected. A simple portkey made from memory to his London flat pulled both Harry and Ginny home without any trouble. Well without any more trouble than they were in anyway, but if you want to hear about how Molly fainted when she found out that Harry and Ginny had had a baby out of wedlock, or how the Aurors office questioned Harry for two whole days about his whereabouts for the last six months without ever getting a satisfactory answer those are other tales.
As for Harry and Ginny, they got married at the Burrow as soon as Molly could arrange it (which was very soon indeed), and that is how they became my mum and dad.