Firstly, I can appreciate the effort this must have taken to get this far. I can see it being useful for a lot of people.
However, the concern I have is that with the house rules added to them, you seem to have partially applied the NPC templates to the base races, but you still treat them as "normal" monsters. I don't think you can do that fairly.
A normal monster would not have a "Daily" power or the extra class features and trained skills, so these NPCs are sort of "half-HP" elites, which I imagine would skew them a noticeable bit in practice. That essentially makes them all "glass cannons" who have great offensive ability but HP as low as standard mooks.
If they have no significantly boosted defenses, no extra HP, and no saving throw bonus or action point, they are basically all unnecessarily complex and damaging monsters who have enough time to use their Daily and maybe their Encounter before they die without giving much sense of their class. On the other hand, they might be able to last an incredibly long time and cause much more trouble for the party than a normal monster of the same level and role, based on power selection.
By comparing a level 5 Dwarf Hammerer from page 97 of the Monster Manual with the level 5 Dwarf Guardian Fighter, you can see the Fighter has a better at-will ability (Tide of Iron vs. a Basic attack), a Daily power which causes ongoing damage and reduces defenses, and Combat Challenge and Get Over Here and also a Second Wind which makes it a much stronger Soldier overall.
By comparing a level 2 Human Bandit from page 162 of the Monster Manual with a level 2 Human Brawny Rogue, you can see the NPC version has better defenses, First Strike, higher Sneak Attack damage, more accurate and potentially damaging at-wills, a Daily power which seriously hinders the target, and the ability to Tumble and a Second Wind. And yet it is given the same XP value as the Bandit.
I don't think you can really have classed NPCs which aren't full Elites, with all that it entails, as a matter of game balance. If you apply a template as you suggest in the Index to make them Elite, all you have done is given them normal Elite hit points and added even more abilities on top of what they already can do, so it's a more powerful Elite as well.
I think leaving them as normal Elites using the normal template rules from the DMG may make for a more practical and useful book.
