The method recommended in the forum for the production process is to have the clothier(s) linked to a stockpile that is linked to the dyer(s) that link their output to yet another stockpile. If the stockpiles are set to "take from links only" you shouldn't get the piles "contaminated" by worn clothes, but as far as I know there is no way to block the dorfs from "stealing" clothing from the intermediate piles, as there is no such setting as "deliver to links only", so dorfs might very well ignore your base quality dyed sock in favor of the newly produced undyed masterworks one.
Given the mess caused by the clothing process as it is, I've never bothered with dyeing myself.
For happiness I think you've come a long way. Tweaking would be to customize their bedrooms with materials/colors/items they like, giving them jobs suitable for them (outdoor jobs for those who dislike the outdoors the least, and who aren't frightened by the green stuff, for instance). I guess not breaking up parties is a good thing as well. Get rid of sentient bodies as quickly as possible, and let the bodies be seen by as few dorfs as possible (if you can micro manage it such that the body disposal is done by dorfs who aren't overly sensitive it would help).
Waterfalls are supposed to be nice (and also quite good at shooting down the FPS). Ah, yes, despite their reputation, dorfs actually like baths with soap (I've embarked in an evil area where it rains goblin blood quite frequently, and they clean themselves as a result).
Trying to ensure married couples work near each other is probably good as well, as it should reduce longing.