A friend of mine I was talking to, who won't be in this campaign, gave me a similar idea as that one Mephisto, which is a good idea.
Here's his idea: (Spoilered due to length)
How 'bout this for the 20ish conjuror; He's looking to fuse himself with something mechanical, having discovered the methods of creating and developing Warforged bodies and started out doing it as an experiment for himself; no big armies, no major conquest or anything of the sort, just some minor crimes against humanity.
However, he's a former worshiper of Wee Jas, who is NOT happy to have such a powerful follower simply abandon worship of her in favor of mechanisms and tinkering deities. Because the conjuror no longer fears death, believing that becoming a construct will grant him functional immortality without the penalties of undeath (both mechanically and fluff-wise since he won't lose a soul, just shift containers), he has essentially rejected her dogma and forsaken his duties as one of her cult. So, she has started sending assassins after him. Failing in that respect, she has begun to usher her other followers to create an army of necromantic powers to strike him down. In a panicked response, what had been a simple experiment to test a theory became an industry, trying desperately to stave off the revenge of a goddess and all the mortal forces she can bring to bare.
I might also suggest that the conjuror take at least a few levels if not all of Ebberon's Renegade Mastermaker to represent the progress he's made in converting himself into a machine (the PrC slowly makes the character into a Warforged over 10 levels with 7/10 casting progression I think. He'll use base warforged as foot-soldiers and high-level golems as his brutes and bludgeons to fight off skeletons and zombies at the low tier and Libris Mortis' horrors at the higher levels.
Meanwhile, the party has only seen the Conjuror's side of the confrontation, and may or may not be able to see through his bluffs that the atrocities he's committing are to stop an undead force that is on its way; he will lie about Why it's coming of course, but there's not certainty that he's wrong either. Perhaps the party was initially contracted by the forces of Wee Jas to help bring him down, and he attempts to reveal to them that they are working for an invader, unwittingly weakening the greatest hope to turn the undead forces away.
Now, this would require him to be using the Renegade Mastermind Prestige Class from Magic of Eberron. That part in particular I love. Its an awesomely-themed PrC, and I'm already a good chunk of the way done creating him.
I'm going to be making some alternative ideas (not set in stone) based on this idea. I like your idea as well, and I will see if somehow perhaps I can include it in there.
First off, I'm making the Conjurer a 15th level Wizard/10th level Renegade Mastermaker. He's basically the most powerful spellcaster on the material plane right now (Or at least in this particular world), as Epic Level Characters are extremely rare. This also means, the players won't have any chance of beating him on their first encounter at level 9-10. They'll encounter him, attempt to kill him before finding out how powerful he is (He'll be just toying with them), before he gets tired and leaves them to their fate at the hands of his second in command.
Now, as for the storyline, this Conjurer is actually not the bad guy. He's just thought of to be. One of Wee Jas's (if I decide to stick with Greyhawk gods, which I might for good ol' times sake) most powerful followers, a Cleric/Wizard/Mystic Theurge Lich, is attempting to fight his way in from say, another continent/the Underdark (Or Equivalent)/Another plane using an undead army, and that the only ones who can basically stand in his way is the Conjurer's Warforged (Will rename) army. However, to create this army of his, he's been committing acts against humanity, as his living constructs require souls to power them, and thus has been kidnapping people to do so. He believes its "For the greater good". The players are sent to investigate these missing people, and end up upon one of the Conjurer's lesser lairs but also happens to be where he is at the time, using a specifically designed construct to kidnap people. The players fight through the dungeon's denizens (I want a good old fashioned dungeon crawl here) and end up teaming up with an Inevitable, who was employed by Wee Jas to assassinate the Conjurer, who himself was once a cultist of Wee jas. She wants to not only kill him because she lost a powerful follower, but also because his experiments into creating living constructs (On himself, first) could be as you said, and so she cannot directly take action against him. The Inevitable is a failed assassin, but was also one of the critical instruments for the Conjurer's success in creating a living construct (Since thats almost what the Inevitables are). The Inevitable is himself uncaring about anything but his mission, but teams up with the players to succeed. (They don't know who he's working for or the exact details, they just know he was sent to execute the Conjurer for breaking his oath to his god)
Now, after the first confrontation with the Conjurer, the players kill his second in command and head back to one of the major cities and get info on him. This, along with assistance from the Inevitable (Who left for a while but came back), helps them figure out ways to sabotage the Conjurer's operations for building an army, which they think he's building to conquer various nations. After they do that, they end up finding a way into the Conjurer's main lair (A demi-plane of his construction), where they are able to set an ambush for him as he returns from a one on one confrontation with the aformentioned Lich. The lich would be destroyed during this fight (But will come back later due to his phylactry surviving). The Conjurer, upon teleporting directly into his lair, is ambushed by the players, and was severly weakened with his fight with the lich. This will allow them to finish him off, only to learn by his near-dying breath why he's doing what he's doing. However, before he can finish, the Inevitable steps in and completes his mission, and seals the Conjurer's soul so that Wee Jas can punish him directly.
Since the players now know their mistake, they may end up trying to contact the Conjurer's General of his armies (Who are now no longer bound to the conjurer and are now free-willed, but believe their purpose still holds true and wish to continue it) to right their wrongs. The General still has control of the machine that can infuse souls into warforged, but due to numerous earlier sabotages by the players, is running low on supplies and "Volunteers". Thats about how far I am in my ideas..
Now, all of this is still not set in stone.. but its what I've been working on the past few days. Whatcha think? Criticism, Comments? I'm all for it.
Note: This is still Pathfinder, despite my apparent heavy usage of 3.5 material.