It seriously helps if you highlight progressively, with more than one shade (sounds like you're just using one. I'd try using at least three highlight colors). Also, try to make every progressively lighter shade more watered down than the last one. If you don't have the patience for that, at least have each layer be sufficiently watered down, and paint multiple layers until the coloring is as solid as you want it to be. This will really help anything from being painfully obvious, and you won't really have to worry about lines being straight. Personally, I can't even draw a straight line to save my life (my hands can get pretty unstable), but this seriously helps. Even if you're just highlighting edges on your model, try it. It will take a while, but it's worth it.
Also: Lay off the late-night coffee-fueled painting! Coffee never helps.