Lyric discussion by 420MuNKEy 

To me, this seems to literally be about jet pilots in the USAF.

"My horse, is a shackled old man, His, his remorse, was that he couldn't survey, The skies, right before, Right before they went gray, My horse and my remorse, Flying over a great bay"

Here I think "horse" is a reference to the pilots physical body, because you generally need to be quite old to be in the Air Force (28+). I think the remorse right before "the sky grey" is talking about a steep vertical climb causing a greyout and then regretting it because his vision is now temporary impaired and he know exactly what he's flying into (if anything).

"Wired were the eyes of a horse on a jet pilot, One that smiled when he flew over the bay,"

I think this is talking about coming out of the greyout and quickly gathering all the necessary visual information and smiling while they realize they aren't in danger.

"My, source, is the source of all creation, Her, discourse, is that we all don't survey The skies, right before, Right before they go gray," I think the first line is a reference to the morality of the pilot. In the second line, I think "her, discourse" is talking about the nature of aerial combat. So it's talking about because of the nature of aerial combat, you can't always know what is exactly where and you might have to pull off a maneuver that would cause a greyout. The rest is as mentioned above.

An error occured.