OK im going to work on these classes because its what im working on at the moment:
Paladin - A technological steampunk mecha-warrior. His steed is an automaton and his armor is fitted with gears and a small engine. A machine in his armor produces his auras, and his holy symbol is a clockwork device that repels undead.
This idea i have addressed already. Building on that, one think i thought about at work today was to make the Paladin class more of a Prestige class, like on the Unearthed Arcana. That might make them seem a bit more important in the image of the Tech. cities. still thinking
Wizard - Like SE, I can see this going either way. But given 3.5's approach to wizards as magicians who use written knowledge rather than inherent abilities, I would go technological. The magic itself could be scientific - I see a staff with vacuum tubes and vials, not unlike an alchemist but with more an emphasis on the usage of energy for spells.
See this was one of those that we were kind of unsure of. Going from the 3.5 approach we decided that a wizard would be more Tech. base because it involves long years of study and practice of the Arcane. i kind of thought that maybe a Naturalist wizard would be something of a Elementalist, or maybe a summoner. I would almost say the best idea would be an Arcana based Druid but we're just having not 100% sure yet.
WuJen - Again, based on 3.5 setting, a technological magic user, but with more eastern flavor. Alternatively, this could be a wild hedge-wizard who relies solely on the elements. So maybe both.
See here, with the WuJen, this was our idea for the Naturalist version of the wizard. Because of their Hermit/witch like nature it seemed almost to fit. They're also very superstitios which actually is incorporated in to their class.
Ninja - A technological sneak who uses chemistry and mechanics to make himself disappear.
SPOT ON!
Swashbuckler - Going naturalist, a boastful warrior like Beowulf but who relies on finesse. Arm with some more primitive weapon than a rapier (a handaxe or even a short spear would play the part) and they can sail a longship as an wandering warrior.
I was thinking along these lines. My original reason for putting the swashbuckler on the naturalist side was for their seafaring fines, both on the waters and land. almost was thinking like a sea version of the ranger

Favored Soul - Innate and untrained says naturalist to me.
unsure with this one. i would agree with you, naturalist, but i want to give it more reason than just "innate and untrained".
Samurai - I'm seeing a variation of the samurai that uses wooden armor plates and armed with macuahuitls. They keep the dedication to honor you'd expect, but don't rely on steel.
i agree with you. Again like above, i want to find more support for them being Naturalist. Honestly i think they could be both, the differece being, with the Techno. Samurai, being the loss of their heritage weapons or something that disconnects them from the original Samurai idea.
Artificer - Depending on how developed your industrial society is, this would be the automaton-repairing folk. But if they're not that far, I might suggest naturalist: they scavenge material they find to create wondrous items, relying more on ingenuity than technology.
I do agree that Artificers Scavenge materials, but they are more magic-tech focused in the Eberron setting. The Tinker, a WoW RPG class, is one i could see going both ways because its very similar to the Artificer in terms of crafting like Mad, but with out the magic requirement, in fact its mentioned in the book that Tinkerer's rarly even use Magic, they make their own "tech-mods" to make up for the lack of Magic.
Archivist - A naturalist shaman who knots her spells on khipu wrapped in coils around her body rather than in the wizard's scrolls and books. Her knowledge comes from experience, stories of ancestors, generations-old khipu entrusted to her, and strange dreams from the gods she must interpret.
i kind of agree. actually your image here gives me a more Naturalist idea of this class. The Tech version i keep imagining involves a cleric-like character, with a lot of reference books. Kind of like a cleric that studies like a wizard, and instead of it being Divine devotion, its knowledge of the world around you.
Monk - Instinct says naturalist, but it's also plausible to imagine a character that withdraws from the noisy industry of a technological society to contemplate and develop their mystical body.
This class is one we have very high disagreements about. On the one had, i agree with you totally on the monk idea. The Argument comes from my friend who thinks a "tech-society" monk would be more of a Matrial Artist, so a monk with out the "monk". He see's them more like Melee focused fighter-est instead.
kind of odd but i can see his point of view on this.
So what are your opinions?
are their any classes you think we should avoid all together? maybe some in other books we need to look into?
maybe another system other than DnD 3.5?
Im open to ideas and opinions and advice.