Wow, thank you very much. That certainly was informative and helpful!
Hmmm...they are way out of alignment. There is a thread here about the angle over the nut and stiffness of action and the concensus seems to be that it makes no difference to the actual "tension" anywhere along the string (just the amount of thension down on the nut.
You may be interested to do what I did to my sustainer strat. When fitting new closed machines to this cheap copy, I got half a dozen copper washers from the hardware store used by plumbers for copper pipes. These washes are fairly thin but the hole is quite wide for the size of them, enough to fit a machine head through...if not they could be filled a littel wider as copper is soft.
So...the E and A string have no washer, the D and G one washer each and the B and E string two washers each. This creates a stagger on a six in a line headstock. I then use one string tree on the B and E which is loosely fitted so that it moves with the string and is really there to add just enough downward pressure to stop sympathetic vibrations. Because it moves with the strings it will not cause friction problems that may effect tuning stability, especially with trem use.
Trem height is a matter of preference and style. By adjusting the neck angle, you could have it set in many ways in relation to the body. As I like Jeff Becks style of both up and down bends, my trems float with significant up bend...on the sustainer strat, the bridge is on a fairly steep angle and quite close to the body in front but with a lot of swing in back. Others like to have only down bends (eg Van Halen) while others block it off completely so there is no trem (eg Eric Clapton).
Having a floating system does mean that normal bending will pull the trem and you will have to bend further as the more you bend, all the strings will be detuning down. With careful techniche, you can rest your hand against the bridge to resist it to make bending easier...but you do risk putting it out of tune (sharp) if your touch is too strong.
To hear the extent of detuning, pluck the low e while bending the high e...notice how as you bend the low e drops in pitch...the amount that this happens depends a lot on the number of springs and tension of the trem set up...if there is a significant detuning, you will find you have to bend a lot further to counteract this to get to a correct pitch...something non-trem guitars do not suffer from.
If you are not familiar with the fender scale or 10 gauge strings, there is a significant difference in the feel of these guitars...they do feel tight compared to a gibson for instance. But the reward is in the tone that the extra length provides. Tremolo's too effect the way bending can feel as described above. A very loose two spring trem can feel very different to something with three springs, even if adjusted for the same amount of travel. I would suggest with ten guage strings, 3 springs are advisable.
So...there is a bit of getting used to, and a lot of variations in setup and this will take a little time, and evolve as your technique progresses or your musical interests change. Guitar Player Magazine ran a whole series of articles where, on interviewing people (santana, Beck SRV, EVH, etc) they would take their guitars and measure everything involved in their set up.
I don't think string trees or any of those things will change the feel and I would definitely try to make the trees so the strings are guided straight from the nut slots to the tuner. My guitar has the original cheap plastic nut and the tuners are non-locking and cheap, but I have no real tuning problems with the set up I described. I do string the guitar with minimal turns and in such a way that the ends are overlaped so the strings are effectively tied in place once tuned.
So...I hope that helps and gives you and others some ideas for set up... pete