by and large: it appears to have a nautical origin:
To get a sense of the original meaning of the phrase we need to understand the nautical terms 'by' and 'large'.
'Large' is easier, so we'll start there. When the wind is blowing from some compass point behind a ship's direction of travel then it is said to be 'large'*. Sailors have used this term for centuries; for example, this piece from Richard Hakluyt's The Principall Navigations, Voiages, and Discoveries of the English Nation, 1591:
"When the wind came larger we waied anchor and set saile."
When the wind is in that favourable 'large' direction the largest square sails may be set and the ship is able to travel in whatever downwind direction the captain sees fit.
'By' is a rather more difficult concept for landlubbers like me. *In simplified terms it means '*in the general direction of'. Sailors would say that to be 'by the wind' is to face into the wind or within six compass points of it.
The earliest known reference to 'by and large' in print is from Samuel Sturmy, in The Mariners Magazine, 1669.
There may be a psychoacoustic reason for why notes of a high frequency are called high and notes of a low frequency are called low.
First, perception.
When high-frequency notes are sounded (from, say, a piccolo or a violin), the notes will resonate in the smaller cavities in your body (such as your head).
When low-frequency notes are sounded (say, from a double bass), the notes will resonate in the larger cavities in your body (such as your chest).
So the higher and lower pitches are felt not just in the ears, but in the higher and lower parts of your body. This perception may have given rise to the terms.
Second, production. In the vocal production of music, singers will shift between head voice and chest voice. Head voice is used for, you guessed it, higher notes. (Think the Bee Gees if you have a leisure suit in the back of your closet. Or your favorite coloratura soprano if you saw Lucia di Lammamore or The Magic Flute recently.) Chest voice, produced lower in the body, produces lower notes.
Third, there may also be historical reasons, dating back well before oscilloscopes.
Research into musical pitches extends at least back to Pythagoras (sixth century BC).
The word gamut come from Medieval Latin, with the root coming from gamma ut, where gamma referred to the bass G and ut referred to the first note in the lowest of the hexachords. (See Etymology online.) As the lowest note, it also has the lowest number (1).
Today, the middle A is called A4 (440Hz for many orchestras). It’s about the middle of the standard 88-key piano keyboard. The A to the left of it (an octave below) is called A3 and has half the frequency (220 Hz).
Could the numbers assigned to octaves from Pythagoras (sixth century BC) and adopted by Guido d’Arrezzo (sixteenth century) have naturally conferred the sense of low to a note? A gamut or G1 is lower in pitch than a G2, corresponding to its lower notation (a 1 versus a 2).
I don’t have enough breadth to know if high and low pitches work in language systems other than those derived from Proto-Indo-European. I seem to recall from Women Fire and Dangerous things that the word anger is widely associated with heat, in part because of the physiological response when one is angered, namely, that the body temperature actually rises. Lakoff’s book may give you some more insight into other linguistic universals.
Best Answer
Shakespeare did utter smells to heaven ... but I am not sure this is the origin of the idiom:
to stink to high heaven. TFD
Etymonline.com says the following:
And there are biblical references to 'smells' and 'high heaven':
I am inclined to go with the etymological reference acknowledging there have been smells, good and bad, wafting to the heavens from mankind since ... the beginning.