[Ned Milburn]

Raising or lowering the saddle puts greater or lesser torque on the bridge, resulting in a different harmonic balance. Usually, to a point, raising a bridge will bring more volume and higher partials in the harmonic balance, whereas lowering the bridge tends to bring the harmonic response more towards the lower partials.

Nut slots should be cut as low as possible but still avoiding undue buzzing. Ie: there should be no more buzzing at the open string than there is on the same string at the 1st, 2nd, and 3rd frets. Nut slots too high will often lead to intonation issues, especially in lower positions, as well as LH fatigue as you identified.

Usually I set up steel string guitars anywhere from about 1.7-2.1mm (high E string) and 2.2-2.7mm (low E string) at the 12th fret. Neck should have no more bow than the thickness of the high E or B strings.