Lets see.
More skill points and class skills. That's good (I fully agree that non-casters should have more skill points, I'm actually making a similar rule in my games, giving extra skills to fighters and monks)
Full BAB. A classic fix. I think a skirmisher should benefit from it as much as a frontliner.
Better AC. In the ends it gets 1 better point than core. So so.
Flurry now has normal flurry, and "partial flurry" that is making your normal full attack as a standard action. I like, simple, and allows monks to attack multiple times when moving, leaving the "full" flurry as full round actions.
Unarmed damage. Hmm. Ends up a bit stronger, yes. I don't know if the increase of dice damage makes it too strong or not.
Bonus feats. Good too, allow better customization. Another rule I'm thinking about using too, giving more feats for non-casters.
Skillmonkey abilities. Not sure about it either. Kinda takes away from the rogue, but seeing as so many classes have it these days, it's not really an issue, just another option for skill monkeys.
Wis and Dex to attack rolls/damage. Made into class features instead of feats. Very good. I could also suggest making it into feats, and have them be bonus monk feats, so you can choose them or pick something else, if you do decide for a high Str monk.
Ki strike. It was increased to be stronger than just "counts as a magic weapon" to actually BE magic weapons. Like having permanent magic weapon/fangs. Considering his role. I wouldn't say it's overpowered.
Wholeness of body. More HP healed with high wis. Good as the Paladin's lay on hands now.
Having Quivering Palm usable by day instead of week is already good. Several times is insanelly good. Considering the difficult to using it, I'd say it's alright. Can it be used in the same target more than once in the same day? I'd say that it should be usable only once in each enemy every day, to avoid people quiverying flurring.
The top abilities that mimic some high level spells. Not sure about the balance, but I think it's flavourful, so I guess it's alright.
DR 20/chaotic seems a bit too much, though. Most DRs don't go past 10/something. You already swapped magic for chaotic, that's good enough
Others abilities being beefed up or usable more than once is a really nice tough.

All in all, I like. Beefs up a monk, and let him do what he should do.

A note on your "ki" or "maneuver" comments. I think they'd work nice with monks, I mean, "Ki strike", "Flurry of Blows", "Stunning Fist", and "Quivering Palm" all does sound like maneuver or ki powers to me. The classes that offer new ones just have better mechanics than the core monk. Your version offers a stronger and more usable class, but offers not many more options than the core monk. It is, as people say, give him bigger number (that we know the monk needs), but more options in combat would be nice.