I'm not exactly sure why you think the Far Realm is a monkey wrench; the basic idea of the Far Realm is that it's the inexplicable/unknown "outside" of the multiverse. Hell, I might even have it that there are actually myriad other planes/worlds in the multiverse of my setting, it's just that most entities are only aware of the base seven (Elemental Chaos, Astral Sea, Mundus, Feywild, Shadowfell, Hell, Far Realm)- that explains where the Brokenlanders and possibly even the Benandanti come from.
Two (I think) new wrenches that came to me on my own have to do with Drow and Dragons (from Io to Dragonborn).
The first and most wrenching wrench is the Drow; specifically, what can I do with them? While there are evil gods in this setting, Lloth is, as far as I know, classified as the Demon Princess of Spiders (yes, I know they use the title Queen, but that's because it sounds better- she's the same power level as Demogorgon or Orcus). As their worship of Lloth, and, by extension, their reliance on demonic magics/demon summoning, is a defining part of Drow culture, how can I 'fix' this given that theocrats of all creeds loathe and despise demons?
One vague idea that comes to me is that Drow are, fundamentally, a group of corrupted elves, but their corruption comes from their fascination with demonic culture. I was thinking that the drow, as a race, are aligned with/servitors of "The Rose Alliance"- that is, they owe loyalty and seek patronage from the demons of both House Astyanath and House Riethii. Forced underground by their horrified kin, the Eladrin and Elves of the surface, they seek to garner power enough to overrun their hated foes, converting those they can and sacrificing those they can't to the appetites of their demonic masters.
This idea, if valid, suggests that the likely "power core" isn't Lloth's priesthood, but basically a union of two demonic cults; The Cult of Pleasure (Riethii) and the Cult of Pain (Astyanath). These are not the 'true power' though- that belongs to a nobility of Drow/Demon half-breeds. The Cults do hold considerable power, though I was thinking that it's at least intimated that this is primarily because their "worship" gives them the most opportunities to father or bear half-demon offspring.
The other wrench relates, in various ways, to dragons. In 4e core, the dragons & dragonborn were made by Io, the Dragon God, whose individualistic/loner nature got him cleaved in half by the adamantine axe of a Primordial, with Bahumat and Tiamat rising from the sundered halves. The thing is, I removed Primordials from my version, so what do I do?
One idea that comes to me was inspired by the Worlds & Monsters' description of how the two halves each embodied opposite traits, as well as by the Ecology of the Lizardfolk article in an issue of Dragon where the Lizardfolk creation myth depicts them as the result of the hermaphroditic god Kecuala, the mate of the likewise-gendered Semaunya, splitting into two seperate entities due to its constant thinking. It basically goes like this:
Io, creator of the dragons, was a strange and powerful god believed by some to have been one of the first to form within the swirling depths of the Astral Sea. Io considered itself a complete entity, for it embodied all things in equal proportion; good, evil, selfishness, generosity, benevolence, tyranny, even male and female, and thus the most perfect. This lead to it being a very individualistic entity, and disliked by the other gods in return for its arrogance. When the War in the Heavens broke out, Io was frequently assaulted, but its great power and legions of dragons (which it likewise considered the most perfect form of mortals, though less so than itself due to having individual genders) meant that none succeeded.
However, it's stubborn aloofness left it at a tactical disadvantage; unwilling to even consider working with a "less perfect" being, it was thus forced to defend its Dominion all on its own, which meant alliances between opponent gods were thus able to steadily gnaw away at the edges of Io's Domionion. This was a source of great frustration to the draconic god, until finally it resolved upon a desperate gambit; even a perfect being could not be in two places at once, but two parts of a perfect being could. And thus it used its power to split into two seperate gods; Bahamut and Tiamat.
For a time, they were able to do what Io could not, but trouble brewed: both had inherited Io's preference for individualism, and worse still the ritual that had created them had made each from opposing traits of Io, which furthered the divide. Finally, the two took to fighting- I'm not sure what over, though I was thinking it might be tied to the loss of Io's dominion. Perhaps it was even this squabble that caused it to *be* lost? Either way, when it was over, the two dragon gods seperated, each taking those surviving dragons loyal to it and retreating to form their own territories. Those dragons who followed Bahamut changed into the Metallic Dragons, those that followed Tiamat become Chromatics.
I was thinking perhaps of tweaking Bahamut and Tiamat some more, just to make them a bit more unique. The most major tweak was that I was thinking of reversing the traditional gender arrangment; in this setting, Bahamut is the Queen of Metallic Dragons, while Tiamat is the King of Chromatic Dragons.
The next tweak, almost as major as the first, is to alter their appearance/title some. I was thinking firstly of making Bahamut the "Mithril Dragon", and thus altering her scale colors- with the Metallic lineup now dumping the copper-alloys for Iron and Adamantine, Platinum doesn't seem so special. Secondly, I was thinking of making Tiamat "The Dragon of No Colors" rather than the Dragon of Many Colors- Tiamat basically appears as a multi-headed drake wrought from solid darkness defined by light.
With the dragons and their patron gods out of the way, my next thought wandered to the new race of 4e; the Dragonborn. Rather than have them be lesser beings created by Io to serve dragonkind, which didn't really seem to fit, I thought to make them a result of the War's end, as well as tying them to why dragons aren't dominating the world.
My basic idea was that, in the beginning, dragons laid great clutches of eggs, like any reptile- this meant a single female could produce up to twenty or more hatchlings in a single batch, which is one of the factors that made them such a deadly defence force during the War in the Heavens. When the War ended and they returned to the Mundus, the other racial patrons beheld this fact and were greatly displeased; at this rate, their own races would be enslaved by dragons, while various gods of nature pointed out such great numbers of dragons would eventually devour all life. In one of the few times since the War that they would come together (the other being the weaving of the Great Curse that makes it so hard to exit from Hell- the relative ease at entering is explained as a "design flaw"), they wove a powerful, mutual enchantment upon all dragons.
To the horror of the dragons, they found their eggs producing not hatchlings, but ghastly creatures that could almost be considered parodies of dragons, creatures that would eventually become called "Dragonborn". The racial gods then communed with the dragons, revealing what had been done: only under certain conditions (precisely what escapes me; any ideas) could dragon females produce true dragon eggs, and only in small clutches. At all other times, the eggs they laid would hatch only dragonborn.
One idea that comes to me from this is that, in equally (if not more so) rare & special occasions, dragonborn females can lay eggs that will produce a dragon hatchling. I'm unsure whether this came as a 'gift of mercy' from the racial patrons, or if Bahamut and Tiamat gave this in an effort to mitigate as much as they could the efforts of the other gods. Also coming to me are the idea of two rituals, which may or may not exist: the first allows a dying dragon to send out its spirit to "possess" the womb of a female dragonborn- the next egg she lays will be a dragon egg, containing the soul of the possessing dragon. This may only work on a blood relative. The other, which definately only works on a blood relative, also allows a dying dragon to send its spirit into a dragonborn, but in this case the dragon essentially consumes the victim, destroying their soul and warping their body into a resurrection of the dragon.
I'm also thinking that this change in fluff might alter the dragonborn society into being matrilinear and with a tendency towards ancestor worship (most "clans" are essentially blood relatives descended from a single given female dragon), but I'm not sure.
Well, that's all I can think of off the top of my head- any comments?