Re: Effect of different p'up heights
IMO it's one of those things best chosen with a screwdriver in hand and a fresh set of ears, rather than set measurements. Depending on the string action, neck relief and the pick attack in terms of how hard you pick. If you go too high, the side effects become obvious. Go too low and other side effects become obvious. Somewhere in the middle lies a sweet spot and it seems best to dial that in yourself based on your hands, and preferences. I generally like them a bit lower than other people and like the treble response to be even in terms of the 5 positions on the switch. Sometimes that means having a slightly lopsided neck or bridge pickup in relation to the other.
There's usually a setting I prefer for clean tones, and another that sounds good for gain.. and it's just a matter of what your main use for that guitar is.. for example, is it a blues guitar, or a high gain rock or metal guitar? It can really help to squeeze the last few drops of tone out of the pickups, rather than buying new ones. Adjustable pole pieces can also be fun to experiment with.