IMO, the smoothing and polishing of wood should be done away with. The quality of wood items would essentially reflect whether someone threw together a stump with a back for a chair vs. a four-legged intricately carved and polished one.
I agree that it should be done away with... for Dwarves, though I'd still like to see it kept around for other races; Humans at the very least, and maybe Elves if they have some thematically appropriate way to obtain the wood.
Just realized you removed the automatic factories after all. 
I still think the prospecting site should be removed, since it does completely change the way you go about mining. (You'll basically be using it constantly, since it doesn't consume anything, and this will cause your fortress to spread out toward the places where rare gems happen to be, instead of being built around your own original design - it also really ruins that lovely feeling of coming across a rare material by chance in the dark, turning mining into more of a hunt.) At the very least, let it require an oscilloscope, like it does for the gnomes (you can buy these in crates from the gnome caravan). That'll keep players from making use of it in the early game.
I would like to upvote IndigoFenix's comment re: mining, in particular the complete removal of the prospecting site for the Dwarves. Lore-wise, this is how I thought of it (clears the throat): the dwarves tear apart mountains and shape their halls through sheer force of will; their ideal praises the value of hard work, the simplicity of picks and strained biceps, ballads of steel and the harsh relief of a brew 'to get through the working day.' Put another way, Dwarves would very much appreciate the legend of John Henry. They'll leave the gadgets to the gnomes, their little buddies.
Re: gems / glass / rock forges: I disagree with the notion that Dwarves would make weapons of
whatever they could, I think that such a utilitarian spirit fits more with Orcs and/or Kobolds. I like the notions of ebonglass/ashland glass and so on, but I don't think think they should be given to dwarves, nor should they have any particular ability to shape glass into war material. Gem forges are fine, though the reagents should be raw gems (I think you covered that elsewhere). Rock forges should be removed from Dwarves, and given to troglodytes whenever they're put in
