This looks like "Deus Ex Homine" by Hannu Rajaniemi. It was collected in Gardner Dozois' Year's Best Science Fiction Twenty-Third Annual Collection, in 2006, which fits your timeframe.
It matches most of your points, as quotes from the story illustrate:
Set in Scotland:
The quiet in Pittenweem is deeper than it should be, even for a small Fife village by the sea. The plague is bad here in the north, beyond Hadrian’s Firewall, and houses hide behind utility fog haloes.
(Pittenweem is a village in Scotland)
Main character is a hacker who used plans on the internet to become a god:
“I was a quacker,” I say slowly, “a quantum hacker. And when the Fish-source came out, I tinkered with it, just like pretty much every geek on the planet. And I got mine to compile: My own Friendly AI slave. Idiot-proof supergoal system, just designed to turn me from a sack of flesh into a Jack Kirby New God, not to harm anybody else. Or so it told me.”
I grimace. “My external nervous system took over the Helsinki University of Technology’s supercomputing cluster in about thirty seconds. It got pretty ugly after that.”
“But you made it,” says Aileen, eyes wide.
“Well, back then, the Fish still had the leisure to be gentle. The starfish were there before anybody was irretrievably dead. It burned my AI off like an information cancer and shoved me back into—” I make a show of looking at myself. “Well, this, I guess.”
Baby causing a wormhole in mother's stomach:
“Yes, Inverness was like a giant Tetris game. Nerds and machines did it. And so we killed them. And do you know what else we saw? Babies. Babies bonded with the godplague. Babies are cruel. Babies know what they want: food, sleep, for all pain to go away. And that’s what the godplague gives them. I saw a woman who’d gone mad, she said she’d lost her baby and couldn’t find it, even though we could see that she was pregnant. My angel looked at her and said that she had a wormhole in her belly, that the baby was in a little universe of its own. And there was this look in her eyes, this look—”
And communicating with a (possibly different) baby:
And then we see the baby.
It is bald and naked and pink, and a hair-thin silver umbilical hangs from its navel. Its eyes are green like Aileen’s, but their gaze is mine. It floats in the air, its perfect tiny toes almost touching the water.
“You only know how to kill gods. I know how to talk to them.” I look at my—son, says the little wrinkly thing between its legs—and take a step towards him. I remember what it’s like, having all the power in the world. There’s a need that comes with it, a need to make things perfect.
“I know why you brought us here,” I say.