Since the marriage was derailed, but so many stories hinge on these two living together, are you saying that Peter and Mary Jane were co-habitating? And that MJ almost had a baby out of wedlock, but (presumably) lost it? In the end, I still plan on enjoying 'Brand New Day,' but I'm curious as to what kind of history these two share now."
The question sort of answers itself when you quoted my saying that "almost" everything happened. The funny thing about the pregnancy issue is that Marvel at the time scrambled to derail the story as quickly as possible. I don't know exactly how that story got as far as it did, but they ultimately realized it was a huge mistake. So, taking that into consideration, I personally feel that that's one that didn't happen, chiefly because Peter and MJ now not having been married, would have taken proper precaution to avoid getting in the family way in the first place.
The truth of the matter is that we're committed to preserving as much of these stories as is humanly possible, but because the marriage is no more and now never was, there are going to be elements that have changed. It's inevitable. But we're striving to keep those ripple effects minor, and you can suss them out in most older stories if you just give it a moment's thought. So Jonathan Caeser stalked a single Mary Jane rather than a married Mary Jane, Norman Osborn and Venom once knew that Peter Parker was Spider-Man but forgot along with the rest of the world, and so on.
Look at it this way: Norman Osborn was dead for twenty years, and then was suddenly revealed to be alive. And that changed elements of all sorts of Spidey stories that had come before it, the entire Harry cycle, the stories where Harry's shrink becomes the Green Goblin, and the whole Hobgoblin cycle. But the details of how this could all work eventually got revealed, for good or ill, and today, nobody much questions the fact that Norman is back and never really died. What we're talking about here is the same kind of thing.
In the case of MJ's pregnancy, that storyline was itself created to end the marriage -- the creators involved only made MJ pregnant because they were planning to reveal that Ben Reilly was the real Peter Parker, and then have MJ and her clone-Pete ride off into the sunset and out of the series together. And it's an element that hasn't even been mentioned in "Amazing Spider-Man" in close to ten years, so it's not an omnipresent element that's suddenly being taken away. It was a turn down a bad road, and some of the creators even realized it at the time (which is why Mary Jane was pregnant for something like two years, as the creative teams struggled to figure out how to write themselves out of the corner they were suddenly in.) So that's an area where we maybe need to squint a little bit more in terms of overlooking it. Or, hey, you can chalk it all up to Mephisto's motivation of preventing Peter and Mary Jane's child from coming into the world.