I have trouble selecting turrets while the ship is moving, I suspect adding more inertial dampeners would make it smoother, but my usual workaround is to cancel whatever order I issued while I fiddle with the ship's gear.

As for mice, I use a two button mouse with no scroll-wheel, and a second mouse as a fake scroll-wheel. I re-mapped everything that would have been the middle button to something else.

E.g. [F] to interact??? Unfortunately [G] (fire all the torpedoes) was a _little_ too close to [F] so ... yeah ... ended up moving the torp button over to [K], which is great until some NPC faction sends me an email and I annihilate the civilian ship which I was asking where their homeworld is. Oops.