Good job, Methuselah Flint!!! Very impressive. I wondered if I could keep the clues obscure enough to keep everyone here from jumping straight to the character who is arguably the series' most significant guest star.
1. I never get tested against a logical opponent.
You said:
"Kirk is not a logical opponent, being physically inferior." Right. And I have always wanted to see what Khan could have done against Spock and vice versa. (I think J.J. Abrams or whoever wrote Into Darkness felt the same way.) We do get a hint in that one of Khan's supermen is fully susceptible to the Vulcan nerve pinch, which I believe only Gary Seven was able to resist (and possibly the Vian as well, in part - he doesn't seem as affected as he could be). But I would have liked to have seen Spock take a few swings at Khan. I doubt Khan had five times Spock's strength, and if Spock can smash his viewscreen as he does in AT, he can probably bend a phaser as well. "It would have been glorious." Still, Kirk does pretty darn well.
2. I directly interact with one primary character extensively, and others less so but still significantly.
You got this exactly. Khan calls McCoy "doctor" on several occasions and calls Spock by his name twice, I believe (both in the briefing room, once in offering Spock the chance to join him and the second in ordering Spock to be taken to the decompression chamber), but he doesn't really directly interact with any of the other primary characters. He's a bit dismissive toward Uhura and doesn't really address Scotty.
3. If one officer had listened to another, I wouldn't have had the chance to offer up such an interesting conclusion.
This is one of my favorite plot-driving dialogue moments in all of Star Trek. As Kirk rushes toward engineering following the release of the gas, Khan has figured out a way to tap into the intercom, and we hear Scotty cut in on Spock's attempts to contact Kirk and say "I'll follow [Kirk] in case - - " but Spock overrules him with the awesome lines (from memory, sorry if this is not exact): "Negative. We must retake the vessel while the anesthesia lasts. Meet me in the armory. I'm blowing it clear first."
Now, Spock's command decision here makes sense. I think he asked Scotty to meet him in the armory because they were going to grab some phasers (maybe even phaser rifles if those still existed) and stun the supermen as a group, rather than assume how long it would take them to recover. I figure they got the weapons, then spread out, with one going to the bridge and maybe the other to engineering. They would need to deal with those left in the briefing room as well (maybe weld the door shut with the phasers? Lock everything there and elsewhere from the bridge after dragging the Starfleet people out to eliminate hostages?) and also the others throughout the ship, because even one of those guys loose could be a big problem. A significant task.
But Scotty, of course (yay Scotty!) was right. If Spock had listened to him and Scotty had followed Kirk - assuming he had a phaser - the climactic fight would have been over fast as long as Scotty could shoot straight. And as awesome as Kirk discovering that purpose-built pipe was, I think Scotty charging in at the last moment to stun Khan several times would have been pretty awesome too.
4. In fact, the sequence of events described in Clue #3 occurs twice, but entirely different officers are involved.
If Kirk had listened to McCoy at the hearing at the end, well, a lot of people would still be alive 15 years later. And poor Chekov wouldn't have been severely traumatized, the Reliant would still be on Starfleet's books, and the galaxy wouldn't have been severely endangered. Good thing Kirk cleaned up that "seed" he planted.
5. To paraphrase James Taylor, deep reds and golds are the colors I choose . . . .
You said:
"The jumpsuit is red, the dinner jacket is gold."
Exactly.

And there's the Starfleet operations uniform they (oddly) put him in also. I always found it fun that they chose red to give him. Because he "was once an engineer of sorts," perhaps?
6. Like some others, I engage in extremely respectful dialogue with the leader of my adversaries, and like many others, I receive the same diplomatic politeness in return.
You said:
"Kirk and Khan have a respectful dialogue."
Precisely! Khan and Kirk are half jerks to each other when they first meet, but after that they are almost thoroughly respectful towards one another in their exchanges. My favorites: "You are an excellent tactician, Captain . . . " // "You have a tendency to express ideas in military terms, Mister Khan. This is a social occasion." And "Do you have any other questions? // "Thank you. They've all been answered." Khan even offers Kirk the chance to surrender before suffocating. And then there's the Milton exchange at the end.
But Kirk does this all the time. He is completely respectful to, among others, Kang, Koloth, Yarnek (apart from trying to punch him and sort of yelling at him at the end), the Earps (again before the punching), the Gamesters, Thelev, Garth, Anan 7, the Proconsul, Vanna, and more who just want to kill him. It's a wonderful hallmark of Kirk's character. No wonder he was able to talk all those machines to death.
7. Curiously, while there are some details about me everyone seems to catch on to quickly, and others remain obscure, my entire set of actions - the first time around that is - are quite honestly enabled by a huge breach of basic security.
You said:
"Bits and pieces such as Khan's remarkable recovery are known quite quickly. His status as a genetically engineered man is discovered a bit later. No security guards are present when he is in sickbay, hence the ability to hide the surgical knife, and threaten the good doctor."
Right on. SS has some enormous plotholes and not one, but two should-have-been-career-ending decisions by Kirk (allowing Khan run of the ship and essentially letting him go at the end), but it's still wildly entertaining and an outstanding episode despite those flaws, which says a lot for the plot, dialogue, action, and acting by the main cast and Montalban and Rhue.
No security guards in sickbay is an excellent point I hadn't thought of; thanks.

The major flaw of the whole episode is that they sort of know immediately that this guy is or must be some sort of genetically enhanced killer out of Earth's past, and instead of locking him up in the brig with eight guys watching him, Kirk lets him read up on the operations of the whole ship, allows him to walk around freely so he can seduce McGivers, finally orders one security guy outside his door who of course turns his back to the door instead of staying at a discreet tactical distance, etc.
8. There were no little puns sprinkled or scattered between the lines in these clues. Until now.
Sprinkled/scattered = "seed" & "between the lines in these clues" = space.

Fun one, ladies and gents, with some great guesses. Thanks! I enjoyed it thoroughly. Methuselah Flint, you have the conn.
