Okay, so the build I'm looking at is as follows:
Dread Necromancer 9 / Ur-Priest 2 / Mystic Theurge 9
Feat selection is
1 - Spell Focus (Necromancy)
1 - Spell Focus (Evil)
3 - Iron Will
6 - Arcane Disciple (Death Domain)
9 - Corpsecrafter
12 - Bolster Resistance
15 - Nimble Bones
18 - Tomb Tainted Soul
Obviously the idea behind this character is a specialty undead crafter. This is my first attempt at creating such a nemesis, so there's going to be some serious growing pains. I want to incorporate some of Saxony's ideas into it, but they seem a bit complex for me to follow (though I am trying). Thoughts on this so far from anyone?
I am willing to re-explain every thing I did to come up with 1040 HD of controlled undead if you want.
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Bolster Resistance is pretty good if your undead will get turned/rebuked a lot. +4 Turn Resistance is basically immunity to turning/rebuking if the undead and cleric are the same level.
If the undead will never get turned/rebuked, its a waste, of course. So figure out your campaign. If the players or DM like using turn/rebuke undead, its a good buy. If turning/rebuking never comes up, its a waste.
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Firstly, Tomb Tainted Soul should be your first feat if you're getting it. Creatures healed by negative energy (All undead and those with the Tomb Tainted Soul feat) are healed 1 point of HP by a Dread Necromancer's Charnel Touch. If a Dread Necromancer has the Tomb Tainted Soul feat, they can heal themselves for 1 point of HP every round. This basically makes them immortal unless outright slain in battle. Combine that with their DR 2 from the Lich Body abilities, and they are actually pretty tenacious spellcasters.
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Nimble Bones isn't super awesome. One has a limited set of feats, so only the super awesome ones should be taken. Of course, if the flavor of Nimble Bones is cool enough, then its awesome level is enough to take as a feat. But I'm of the opinion that there are both more flavorful and more powerful feats out there.
Instead of Nimble Bones, I'd go for Destructive Retribution (Also a Corpse Crafter feat). you should look up the details in Libris Mortis, but it basically says whenever one of your undead die, they explode in a negative energy burst dealing HD/2 d6's of damage to living targets if they fail a reflex save or healing that much to undead targets. So if a skeleton had 14 HD, they'd explode, dealing 7d6 damage to everyone around them.
If you have a horde of undead, when each time one of them dies the others get healed and of course whenever one dies, they deal additional damage to living targets around them.
A super cheesy trick to animate a bunch of bats. They have 1/4 HD each. But they still deal 1d6 damage with Destructive Retribution (since its the minimum). So one takes the Tomb Tainted Soul feat and then whenever they want to get some healing, they just munch on some undead bats to feel better.
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Look up the "Otyugh Hole" in Complete Scoundrel (page 151-152). It costs 3,000 gp and takes a week to use. Using it grants the Iron Will feat for free! That's awesome for a character that wants to go into Ur Priest.
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I've heard that Spell Focus (Evil) and Spell Focus (Necromancy) don't stack when a spell is both an Evil and Necromancy spell. And a lot of Necromancy spells don't give a save so Spell Focus (Necromancy) isn't as good as Spell Focus (Evocation), for example.
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For your Advanced Learning spells at level 4 and level 8, here are the spells I think are the best:
1st/2nd level necromancy spell: Desecration (Players' Hand Book, Cleric 2nd level spell) is of course great for a Dread Necromancer. Ur Priest will eventually gain it as a cleric spell, but if you don't go Ur Priest you will need Desecration somehow. And maybe one doesn't want to wait until Ur Priest to use it. It's a very good spell for those who use Animate Dead.
1st/2nd/3rd/4th level necromancy spell: Burning Blood (Spell Compendium, Sorcerer/Wizard 4th level spell) is a GREAT debuff spell. It lasts for rounds/level and if the target of the spell fails a fortitude save on any of those rounds, they are limited to only a move action (they can't attack or cast a spell because that requires a standard action) and are dealt 1d8 fire damage and 1d8 acid damage. The damage is poor, but the action limiting is awesome for shutting people down. The best thing is, a successful Fortitude Save does NOT end the spell (unlike Hold Person).
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I would stress to you that you should replace the second level of Ur Priest with a level in Contemplative (also in Complete Divine). The second level of Ur Priest just grants Rebuke Undead (which Dread Necromancer already has). So it doesn't give much. Just two more rebuking levels which stack with Dread Necromancer's Rebuking levels. Since you're already taking levels in Mystic Theurge (which doesn't advance Rebuke Undead) you might as well have a Rebuke Undead level of 1 because you will have ZERO chance of affecting undead with HD comparable to your character level and most undead have HD WAY higher than their challenge rating. This means even characters with only Cleric levels have trouble turning/rebuking some undead and you're already very behind them.
So the loss of Rebuke Undead from Ur Priest really isn't a loss.
Contemplative (Complete Divine) gives you a Bonus Domain of your choosing and advanced Ur Priest spellcasting. That's worth a lot for an Ur Priest who has few spells per day. It's effectively 1 more spell in every spell level that the Ur Priest can cast. Of course, they also get the Domain Ability in addition to the extra spells.
So just look up Contemplative in Compete Divine and make sure you qualify after level 10 and see what it adds to your build. (Your build will qualify and it adds a lot
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That 9th level in Mystic Theurge doesn't make any sense. Ur Priest only has 10 levels. So you can't have 2 levels in Ur Priest and 9 levels in Mystic Theurge ( or 1 in Ur Priest, 1 in Contemplative, and 9 in Mystic Theurge) because that adds up to 11. There's no 11th level of Ur Priest to get spells from.
So just take an Arcane Spellcasting class for 2 levels at the end. You still get all 10 levels in Ur Priest, but you can also get some abilities from other Prestige Classes that you wouldn't get if you took the 9th level in Mystic Theurge.
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I like your placement of Arcane Disciple. It's an obvious buy for a Dread Necromancer/Ur Priest/Mystic Theurge because you already have a high wisdom for Ur Priest spells. I'd take it at a lower level so you can have access to the spells right away. Taking it at level 18 would make much sense because most of the 1st, 2nd, and 3rd level spells would be totally useless and thus its less useful. Taking it at level 1-6ish mean you get to make use of every spell given by the feat.