Dead Boy traded away his original name as part of his deal.His name obviously wasn't always Dead Boy, but that's all anyone ever calls him and no one acknowledges that he was ever called anything else. He may not even remember what his original name was.
Dead Boy made his deal with Lilith.Dead boy never says who he made his deal with, saying something along the lines of worse than the devil and Lilith was hanging around the Nightside for the past 30 or so years in disguise.Any coincidence that when dead-boy made his deal is around the time John was born (John's ~30 years old).
Lilith did something truly torturous to the Detective Inspectre in the Bad Future.In Hex and the City, John overhears the Bad Future's Larry Oblivion wishing he'd died for real, like his brother Tommy, rather than (un)live to see the Nightside brought to ruin. If Hadleigh Oblivion had also been killed outright, Larry no doubt would've wished he'd died like both his brothers, which rather implies that the eldest Oblivion brother met a fate even worse than Larry's. Lilith's minions probably weren't strong enough to take Hadleigh down by themselves, which means she more than likely defeated him personally.
The good angels only repaired the damage their side had inflicted in the Angel War.Jude suggests that, because they are the good ones, the hosts of the Shimmering Plains would repair the destruction and injuries the Angel War had wrought, although restoring the dead to life was beyond their power. The next few books, however, establish that the angelic invasion did have a lasting impact on property (e.g. the Cavendishes' financial loss from destroyed real estate) and people (as with Count Video needing to have his skin stitched back on). This doesn't necessarily have to be a Canon Discontinuity, if Heaven's angels only repaired the harm they had caused, leaving whatever destruction Hell's agents had wrought for mortals to clean up.
John is the Could've Been KingWe know that the Travelling Doctor is a regular visitor to the Nightside. We know that there were many horrible things sealed away in the Time War, and it stands to reason that the Nightside is one of the few places they could cross over. Now this one requires a bit of a stretch, but we've seen John grab things from alternate timelines. Is it possible that, in the Bad Future, he became the Could've Been King, and his army of Meanwhiles and Neverweres are things pulled from side timelines? On another note, a Dalek invasion of the Nightside would be a trip and a half...