I'm sorry it took so long to get to this. Scatterbrained author syndrome mixed with two Thanksgivings, a midterm, and an incontinent dog, I suppose. Anyway, the point is I finally got to it, and wow... If you're really as new at this as you say you are, you've got a hell of a bright future.
Okay, my notes:
A really great start! You can certainly tell you like hard sci-fi. Right off the bat, I have a suggestion for you: Start submitting your work to Interzone and Analog. Those are the two sci-fi magazines out there that really eat hard sci-fi up. Interzone, especially. The editors there are on a mundane sci-fi kick right now, and WHAT YEAR IS IT falls right into the category they're looking for.
I can tell you're educated from your writing. VERY well so. In fact, you have a tendency that almost all very well educated scientists/engineers/physicists have when they write: They sacrifice the character for the setting. This stood out the most with the perfect Christmas train scene, where the protagonist proposes. Things were...well...too perfect. They were very cookie-cutter, leaving both characters feeling hollow. Like I said, this really is a trait that a lot of science and math-minded people have when they first start writing.
Ways you could have made the characters more empathetic? Easy. Have the protag botch the marriage proposal. Have him fumble and stutter, have the train explode, the ring fly up into the tree, the rug catch on fire...and have her accept anyway. That makes both characters sympathetic at the same time--him for being a clod and her for loving him anyway.
Another tendency that scientist types have (I'm not bashing scientist types, btw. I thought your worldbuilding was FANTASTIC, which has always been my worst quality) is that their characters think too much. Instead of having an "Oh, s***" moment when things all suddenly fall into place for them, they've already pieced the entire situation together by the time they've sniffed the atmosphere and decided it's 30% carbon dioxide, which suggests that someone has been breathing it for a few millennia despite the ship's sensors saying there's no life on the planet, which means someone is hiding underground and therefore is probably afraid of them... See what I mean? Analytical reasoning can be a very bad thing when you're telling a story, at least when it's going on in the character's head. When the character deduces everything logically, you're not giving the reader a chance to EXPERIENCE the fleeting moments where the characters sees someone running in the shadows, realizes there's too much carbon dioxide to be natural, and then has a holy s*** moment where, Gee, I'm six miles from my ship and I'm not alone out here, am I?
Those holy s*** moments are the gems of writing fiction. If you weaken them by giving too big of hints aforehand or by having your character deduce exactly what is going on and skipping the holy s*** entirely, then you're skipping out on a really powerful moment in your story.
An example of this would be when you write this:
"What doesn’t make sense is, I was scheduled for a five-day freeze and it would take years to grow fingernails long enough to curl under like rams horns."
What you've done here is you've already pieced it together for the reader. However, I can assure you with certainty that the reader had already picked up on that long before you said it. That's another thing you want to avoid--sounding like you're spelling things out for the reader. Sometimes (not with your work, but it's a danger) it can sound condescending if you tell your reader what to think.
So to use the same example, as an editor, this is what I'd change:
"I was scheduled for a five-day freeze. Why are my fingernails long enough to curl under like rams horns?"
And then let the reader piece it together.
OK, moving on: I LOVED your curled fingernails making the guy think he was seeing spiders. That was a PERFECT way of showing, not telling. You were showing that he was hallucinating by having him have a panic attack and slap at spiders, not TELLING us that he must be hallucinating because spiders didn't really grow that big. Great job here! What I'd suggest is try to apply that more liberally to the rest of your story. Have things happen that he doesn't understand, and then when he figures it out, doesn't go back and explain because the reader's already figured it out with him.
Technology: DAMN this was good. I loved (loved, LOVED) the way you detailed cryogenics. I seriously think that if you cleaned up your style a bit, you could make some sales to some really top-notch magazines. Your worldbuilding was kickass. Kudos on that.
Plot: This is a toughie. Quite frankly, the editor in me would tell you to cut the flashback entirely and focus on the protagonist accomplishing a goal before ending the story. This is the essence of a short story. This was, in my opinion, not a short story, but instead the first chapter of a novel.
A short story is like a novel, but a HELL of a lot harder to write. It's gotta have a beginning, a middle, and an end. That means a character has to be faced with a problem right off the bat (in this case, waking up an old man) that he finds a reasonable solution to BY HIS OWN MEANS (a lot of people don't like that one, for some reason...the hand of God is too tempting somehow), thereby accomplishing an overall goal.
I saw your overall goal, definitely. However, I didn't see a solution. If you're going to try to make a sale to one of the big names, you're going to have to work hard on that part.
Extra characters: There's a couple unofficial rules for short stories I like to follow... If it's a short story, it's got one main character. If it's got other characters, they die off. No reason to have more than one POV in a short story. You simply don't have the space. Every single word counts, and if you can tell the same story through one set of eyes instead of two, do so.
HOWEVER, as a novel, the added characters are a must. The protag's gotta have someone to interact with, someone to mourn, someone to betray him, someone to piss him off. In essence, I really liked the characters you introduced (the woman, especially. You had me grinning when you introduced her as a Captain...can we say conflict?) but I think you need to look at them with a critical eye and decide just how much of the story you're going to dedicate to the group and how much of it you're going to dedicate to the plot. If you're gonna keep it short, the plot is all-important. Remember (you aren't gonna believe me until you're staring at your first stack of rejections...it was the same with me), every word counts.
Okay, whew. Let me end with the fact that I thought this was superb to be your first piece. You've got a long way to go, but you're already ahead of the game in a lot of ways. And remember about Interzone and Analog. Someday, I think you're gonna find a home in one of them.
And one more thing: I AM an editor. I do this for a living. I see dozens of stories a week. Rarely do I see such a wonderfully detailed technological world, so I really am serious when I say you're on your way.
Good luck, and be sure to check out those magazines! (If I had to pick one that best matched your style, I'd say start with Interzone first. They're much more blunt about their rejections, but their content is a lot closer to what you're writing. Just don't let them hurt your feelings. When I was first starting, I almost quit because one of their rejections came back saying my story was boring. Yee-haw, right?)