Well, to tell the truth, there is not much left to do in Graniteprison after 8 years.
I'm trying to keep my fort lean and mean to keep the FPS up. No clutter, no extra rooms, no crafts for trading. I religiously atom-smash and trade away anything I don't use. Minimal flowing water, no cavern exploration, no flowing magma. I only stockpile food, metal bars and leather.
I pretty much have at least one legendary dwarf for every workshop I use and everybody is wearing decent armor, iron for the military, iron and leather for the civilians.
The last project was a "waiting room" for invaders so they don't run away before I have time to take care of them:
The damn gobbos send a small squad of brainwashed dwarfs... It was over very quickly. D:
Right now I need to find a new project that doesn't hurt my FPS (too much).
I didn't have any problems with bad thoughts. I got plenty of booze, lavish meals, everybody gets an engraved 4x2 bedroom with nice furniture. My legendary engraver covered everything with masterwork pictures, every dwarf is wearing a very expensive set of armor and a masterwork sword and I think once they become legendary fighters they don't get bad thought from training or being stationed anymore.
I put the Captain of the Guard accidentally on pumping duty unfortunately but it's not too bad. He's still very weak. Besides, most dwarfs are heavily armored and clad in iron armor (no flux) so they should be alright. xD