This is very, very well done. I had my doubts when I saw how long it was, but I really enjoyed reading and critiquing it. Very intriguing characterization and transitions from past to present. I liked it a lot.

So I'll go through bit by bit to make comments and suggest some small-scale changes:
"A golden eclipse was emblazoned upon the back of his eyelids." - this is a really cool beginning, I like it a lot.
"The crisp, morning light, an event horizon on the surface of his vision." - I don't really understand this sentence, and it feels like a fragment.
"Untying the Gordian Knot is either a complex puzzle or a simple chopping manoeuvre." - I suggest changing this to, "A Gordian Knot can be untied by a complex puzzle or a simple pull of a knife." or something like that.
"his day or reckoning, as it were." - I suggest taking out the "as it were."
"He'd been taken hunting in Maine, at February time." - this sentence is unnecessary.
"A black mark at the end of your life, such as pleading for it, marred your time in the world." - I suggest taking this out too.
"as most people" - "as most sons"
"He'd went" - "He'd gone"
"neither his absent mother." - "nor his absent mother."
"the golden colour of the sun dance its merry dance." - the way you described it before did not give me a "dancing" vibe... it was calmer than that. This first section has some really ace characterization. Great job.
"as if he were any other man." - take that out.
"This box contained the only possessions he owned, or at least had access to." - make a decision: are they the only possessions he owned or does he have more?
"hand written" - "hand-written"
"even teenagers," - take that out.
"Not that he'd cared, high school, if not his entire teen years, were spent entirely alone." - change the comma after "cared" to a colon. The last paragraph of this section is a really good segue into the next section.
"Goosebumps" - should
"destined from Kindergarten" - I suggest changing it to "destined from childhood"
"American's" - should be "Americans"
"He pulled the old revolver, more of an antique than a weapon, round in an ark and fired. The 1944 issue gave a kick that dug right into his shoulder, nothing like a rifle. The force of it knocked him back off of his feet and keeled him in a circle, pushing him back into a sitting position." - I would change this to, "He pulled the revolver given to him by Eddy into the air and fired without thinking." and the revolver is a hand gun, right? so why would it slam into his shoulder?
"There was one sweet moment of hope when it looked as if it might pass her by." - make this "when he thought he had missed."
That scene is really well done.
"After all, the birds don't sing when you're six feet under the soil." - change "soil" to "ground"
I suggest introducing Clara and his son earlier, because they seem rather important.
"Share the wealth like you share the love, his mother used to say." - take out the "the"s.
"It caught the sunlight from his window," - change it to "The ring caught the sunlight from his window,"
"none-the-less" - should be "nonetheless"
"He'd been named" - change to "The man had been named" because I thought you were talking about John.
"He'd once told John that he'd only carried on running and shooting because he'd presumed the death sentence had already been decided upon." I love that.
"She'd moved away somewhere upstate, leaving Two-Timer to fester, alone." - consider changing this to "leaving Two-Time to die alone."
"Yet, he was determined not to be one of them." - take out the comma.
I think you should uncapitalize "Warden" but that might be just me.
"Time to say fair well." - should be "Time to say farewell."
"It was time to..." - take that out.
"Inmate" - should be uncapitalized.

Great ending. Keep up the good work!