What's good big pimpin', I just read through this. My feedback is as follows:

First let's take a look at your opening, and let's see how we could improve.

This morning when I woke up, I didn’t think things could get worse.

Instead of using 'thought' verbs like think, believed, felt, I always try to instead expand upon what exactly it is that is causing the character to think or believe or feel something. So rather than 'The teacher believed Roger was cheating.', it would be 'There was often movement in the third row, second seat, where Roger Rimrock sat. But whenever the teacher would snap her head up, Roger was always straight as a rod. Something was up.'

However, this is a short story, and you obviously weren't aiming for a ton of wordcount. In a case like this, I would honestly drop the second half of the first sentence entirely. It would read like this:

This morning when I woke up, at the foot of my bed, was a guy I'd known all my life.

And then continue on just the same from there. We don't need our protagonist telling us he didn't think things could be worse, because finding Gus dead and soiled at his bed says it all for him! Stronger, and more immediate. In the same paragraph there's one of those 'thought' verbs again right here:

I knew he was dead because my favorite pen, the one my ex-girlfriend had given me the birthday before she found me and her sister in a parked car in front of her work, was sticking out of his right temple and there was shit in his pants. Cold shit.

Again, just drop the icky and unnecessary thought verb.

My favorite pen, the one my ex-girlfriend had given me the birthday before she found me and her sister in a parked car in front of her work, was sticking out of his right temple. And there was shit in his pants. Cold shit.

That gives the reader everything they need to know without being spoon-fed.

She seemed surprised, but she agreed.

This is another one I'd 'un-pack'. Again, I get it, short story and all, but it's good practice if nothing else. Give us a specific detail that'll clue us in on her surprise without outright telling us.

When I came to, a doctor was checking my chart.

I actually like the way this paragraph reads better without the phrase 'When I came to,' Again, there's more immediacy without it and the ensuing details will clue us in on our narrator's previous unconscious state. A few other notes on this paragraph:

A doctor was checking my chart. I had a headache like I’d been slapped by a whale. I had no idea what happened to me, but hell or high water, I was going to get myself a pint of Harpoon. There’s a whole lot of strangeness in the world and I’ll be damned if a cold pint can’t go toward fixing them.

A lesson on similes and clichés. Anywhere you can use a simile, a metaphor is usually stronger. This is a lesson I learned from those old Chuck Palahniuk essays on writing, in fact. So, instead of 'I had a headache like I'd been slapped by a whale.', it would be 'My head had been walloped by a whale.' Stronger. Too many little comparisons distract your reader and they're usually too weak to make much of an impact. In fact, just avoid using the word 'like' to compare two things in your writing in general.

As for 'hell or high water', this is a less important note than simile usage, but good to note nonetheless. Idiomatic phrases in small doses are usually pretty safe, so you're fine here. But, for practice, instead of using these packaged cliché phrases everyone knows, phrases like 'hell or high water' and 'a blessing in disguise', try re-inventing the world in a way unique to your character. Give them their own 'burnt tongue' and made-up idioms to use... because real people do that! This is an easy way to characterize people and make your story feel fresh and unique. Often times I'll go through spotting every idiom I slipped in on autopilot and replace them with phrases and verbal tics unique to the character. The result is almost always stronger writing.

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Something that worked for me in this story were the interactions you had take place between the characters. They were snappy and moved things along without being too wordy. As thenewgreen mentioned, this was very noir and that's always a fun, sexy setting to play in.

Keep writing.

It's funny that you brought up petit mal seizures lil. It reminds me of this story, which is kind of long but interesting nonetheless. Last year I had a friend come into the city to visit, a friend from high school. She was traveling with a roommate of hers. Before they arrived, this friend of mine called me informing me that her roommate was an epileptic and suffered from frequent petit mal seizures and in the past had two grand mal seizures. She said it was nothing super serious and that she could handle herself but wanted to let me know up front. I had very little experience with epileptics in the past--I knew of only one boy my age who graduated in my class. He was an epileptic and an outcast in highschool, a loner. He had a splotchy red birthmark across his face. I always felt bad for him, and once or twice he had a seizure in class. It was pretty frightening to see.

So my friend and her roommate finally arrive in the city, and before meeting up with the two girls I felt increasingly apprehensive about the whole epilepsy business. I didn't know why. It was no big deal, right? But I couldn't shake the images of that boy with the birthmark in my highschool graduating class, twitching on the ground next to his desk with his eyes rolled in the back of his head.

We end up meeting outside of their hotel on the street and her roommate seems completely normal, as far as I could tell. Of course! What was I expecting... She's an epileptic, not some fragile alien life form. My nerves settled. We grab coffee, walk around the city for a bit, hit the market. The girl was extremely funny and made light of her disorder like it was no big deal. Every two minutes or so her eyes would flutter and she would zone out--a petit mal. Each one only lasted a split second though and then she was back to reality. That night the three of us were at my place and I couldn't help but grill her about it. She answered my questions very politely and even seemed enthused to be educating someone on her disorder.

The next day, my friend had planned to spend alone with her sister, who also lived in the area. Her roommate had nothing to do, really, all alone in the hotel. So I offered to take her out for the day, show her around the city. She agrees and we meet outside the hotel once again. We walk for a few hours aimlessly around the city until the girl stops dead in her tracks. Her head was tilted up and her arms hung by her sides. But it wasn't a seizure she was having, she was instead entranced by the building in front of her--a dance studio. She ran inside and disappeared behind the glass doors without saying a word and I chased after.

Inside of the studio there were long, expansive mirrors that stretched way way down, and a bannister that ran alongside. The floors were lightly dusted hardwood and there were a few couples practicing ballet out on the floor. The epileptic roommate already had her shoes off and was about ready to run out onto the floor when she grabs my hand.

This girl could move. Her body was long and slender but she had power and balance to boot. After a while I just stopped dancing (if you could call it that) and watched her go. It was like seeing an entirely different person. She moved without stutter and her arms and legs just flowed there in front of me. Seriously, I had never seen anybody dance like that before in my life.

After she wore herself out she sat on the dusty floor with this huge grin on her face. She told me that dancing was the only way she could think right, moving was clarity. And the best part about it all? No seizures when she danced. Not one. How strange and wonderful, I thought. I always wondered what it would be like to suffer from this terrible disorder but have this one escape, this one thing you could always turn to and be free. I was amazed.

As far as this story goes, the feeling of disconnect between our protagonist and the world is very real, and I'm glad you picked up on it. He's 'different', all right... If I were to expand this, I would most definitely try and find a character he could connect with, as you said. Maybe someone just as 'different' as him...