As far as fore and aft saddle position goes, a plumb line dropped from the head of the tibia (the hollow to the inside of your knee cap) should pass through the forward pedal axle with the cranks horizontal.
As far as saddle height, the rider should have a 15 degree bend in his/her knee with the heel down and the pedal at its bottom most position.
I didn't make this up: I paid good money to one of the world's premier bike fitters for this information.
Upper body position depends on the type of riding and the type of rider.
For riding on the track, the rider wants the most aerodynamic position possible, which means back parallel to the ground.
In order to ride in this position with any power, one must move the saddle far ahead of the position I described above.
In other words, normal rules of fitting don't apply to the track or other forms of bicycle racing.
For the street, one can determine the best upper body position for one's self in the following manner:
1. stocking feet or bare feet;
2. sit on a hard chair on a hard floor (no carpeting);
3. place the feet together under the forward edge of the chair;
4. extend your arms forward for balance, and slowly begin to stand up; and,
5. at the very instant your bottom begins to break contact with the chair, note the angle of your torso.
For riding on the street, with no aerodynamic considerations, the angle of your torso, as discovered with the above method, represents the best torso angle for you (and no one else).
Younger men and women will break contact with the chair with their torso much further forward (more parallel to the ground) than will an old guy like me.
However, I don't really ride that upright.
My normal hand position on my bullhorns actually falls a little below the height of my saddle.
Younger folks, though, can ride comfortably (and more aerodynamically) with an even lower hand position.
This natural torso angle (which varies from person to person) makes for more power and agility, and the ability to look around comfortably in traffic.
As for the distance of the handle bars from the saddle, I recommend borrowing as many different angles and lengths of stems as you can and just experimenting until you find a stem length and angle (and a grip angle) that doesn't cause neck pain or hand pain.
You might also need to add or remove spacers on your steerer if you ride with a threadless headset.
Experiment, and when you find the right combination you will know immediately.
For me, the stem that gives me comfort has a 90mm length when my bullhorns have a slight rise to them.
No hard and fast rule governs the distance of the handlebar from the saddle, nor its height.
This varies from person to person.
And, again, those younger riders who put speed and aerodyamics ahead of comfort and agility might accept or tolerate a more horizontal body position.
That said, for one's knee health when riding on the street, try the rules I posted above for positioning the saddle.