9 prestige classes are a lot to comment on, and I haven't assimilated most of them yet. But I've done some thinking about a few of them, and here's some feed-back. Hope some of it might be useful:
Maybe I'm not reading the document correctly, but I don't see what is special about the stenourgos (cool name, btw). Wouldn't the Energy Substitution feat be an easier way of getting a lot of sonic spells? Improved listening and sonic resistance are nice (though they contradict one another- are you more sensitive to sound, or less?), but not, IMHO worth sacrificing 7 levels of spellcasting.
I think the Kosimancer might be a bit on the powerful side. Compare it to the Candle Caster- candles are hard to light and (until 7th level), don't take effect until the next round. Gems don't have any such limitations. On the other hand, those gems are pretty expensive. Is there any way of making them have 10 charges for 1/5 the cost?
Flavor-wise, I think that you could get rid of the verbal component of activating them, but you should keep the somatic component. You should have to gesture with them, or at least point them, for them to release their magic effects. I am correct, I hope, in thinking that "Triggered Gemstone" makes it work like a wand, and thus you have to move it around and say "Bibbety bobbity boo" or "Ala Kazam" or something.
If I were introducing it into my campaign, I would probably put in the Silent Activation ability, and maybe "Capture Brilliance" which lets the device use the ability modifier of the user, and maybe bonuses due to the caster's feats, too. In exchange I would drop obedient and universal.
Eye of the Dragonkin is great. I would assign the gemstones a little differently, primarily so that you don't need an eye-ball sized piece of diamond to get a focus in Transmutation. Instead, I would use a pearl (the transformation of a grain of sand into a pearl is a fine symbol of Transmutation, I think.) Cat's Eye Chrysoberyl for Divination ('cuz it looks like an eye), amber for conjuration (cuz bugs are sometimes stuck inside), jade for abjuration (cuz its a very hard substance, suitable for a protective item)... the reasoning for the others goes downhill a bit- mostly I looked for contrasting colors. For example, emerald and topaz were out, because we already have jade and amber.
Your Lord of Time class is fantastic, probably the best "Chronomancer" class I've yet seen. I think, though, that the Latin is a little shaky: it should be Dominus Temporis, or Domini Temporis in the plural. Tempus is not a 2nd declension masculine noun like dominus is- it is a neuter third declension noun that undergoes a stem change.
I'm still thinking about the Disciple of the Arcane Fist. I suspect that the spell ability more than makes up for what the disciple sacrifices to enter the prestige class. Lowering the hit dice to d6 would help. I'm not sure.
The rest I mostly haven't looked at long enough to give any definite feedback. But I am very impressed with what I see so far- even when I quibble on certain minor details, the elegance of the classes is superb.
