Morpheas to the rescue! YAY!! 
Just kidding 
I'll try to keep it short, but this WILL be a long post, so excuse me in advance.
First of all, a couple of questions:
D: I'm... not so sure about that, I think it's mainly because of the drug issues (Hannah is semi-addicted to painkillers) and her past experience concerning Travis with that.
Vicodin! Just kidding.... 
Hmm, why does Hannah use painkillers, is she affected with some chronic pain disease? Just curious here.
And what about her past experience with Travis? Isnt he Mish's BF? We dont know all the little details here in the Chatroom, so thats why I'm asking! 
H: Add Speed and Pot onto that.
"Speed"? What is that?
Now, I will try to keep my personal experiences out of my evaluation/opinion on the matter, considering that I did have a similar experience, so here we go:
The... relevant parts of the conversation are listed, the rest is me trying to figure out what " But I see you more as a brother than a potential bf." means. I was absent on Tuesday for a physical at the doctor's, but she did text me after school, asking where I was and stuff. There was a joke about incest, referring to her and I dating, but I can't recall the circumstances of it.
Well, it is obvious, duh
If she is being honest, then she said that she sees you more as a good friend (brother), than a guy/potential BF. I dunno, I will have to hear more about that incest joke, to have a better opinion. It depends on how much you know and trust her. Would she lie to you about something so significant?
Now, I wanna stay in the part where she pulled you away from your friend, hugged you, and said "Koda your girlfriend isnt here, give me a hug.". Emphasis on the "girlfriend" part. If she looked at Mish as competition to the whole dating thing, ergo if she wanted you to be her BF, and get rid of Mish, I think that she would call her with her name (Mishayla).
Like saying: "I'm your girl friend who's almost like a sister, and Mish is your GF. Now that she isnt here, we can hug, without her being jealous."
It might mean something else as well, but this is how I see it. But it definitely means something.
Have you tried not letting her hug you to see how she will react? Do the experiment sometime, if you want.
And what about the whole "brother-sister" thing?? Are you and Hannah really that close as friends? Tell us more.
How do you know that she would have kissed you if you didnt have a coldsore? Did she make a hint or move that made you think that? Or is it a wild guess? And by kissing you mean cheek to cheek right? Otherwise its "making out".
Today, Mishayla comes back, and aside from being exstatic to see me for the first time in a week, is noticably angry at me for getting a coldsore (After I drop her off from first period, I try to walk away, but she pulls me back and tries to kiss me, but I regretfully inform her that I have a coldsore. 1/2 Dissapointed 1/2 Irritated, she lets go of me and walks into class), but aside from that acts as though I'm the last beam of sunshine in the night sky, and savors my every second with her. (Something I do enjoy very much )
Ok, now why would she be angry at you for getting Herpes? I mean, you didnt do it on purpose obviously 
However, her infatuation with you is definitely a good sign, if not something more.
Hannah, as expected, avoids me whenever Mish is around, acting as though the past few days never happened (she even told me to keep the fact that me and her text a secret... again, concerning),
I would advise you against that. Seriously now, it is a lot better for Mish to hear it from you, now that it is early, than her finding out the wrong way later on, when you will be closer with her.
Secrets in a relationship never help anyone. Neither the secret-holder nor the person who doesnt know.
Me and a friend of mine, Miranda (a psychoanalist as much, if not more, than I am, she always tries to pry out of me whether or not I have feelings for Hannah, of sympathy or otherwise, in our conversations) and she concluded, based off of the above, that Hannah has an emotional and physical hole left in her where Mishayla used to be, and that she's attempting to fill the hole, primarily with me, but also with overly flirtatious acts towards strangers (At homecoming, for example, she danced with 3 different people, two girls and one guy, and she later bragged in front of Mish that she gave the guy a hard-on). She did not, however, directly answer my question about Hannah's possible romantic feelings for me, rather, she tried to figure out what my feelings were towards her.
Psychoanalists, psychologists, psychiatrists, cant really tell a person who they really are, or what they feel exactly. They can give a pretty close evaluation or analysis at best, but they cant be sure, and certainly cant be precise.
Now, Miranda's analysis might be correct (as much as it can be), but the only way you can be sure, is to ask Hannah herself.
Question: What is a "hard-on"? I assume its erection expressed differently? 
1. Mishayla is jealous of any girl that interacts with me (At homecoming she was laid-back about this, since she didn't want to pressure me into anything, but she did keep an eye on any girl that approached me after Tawnee started dancing with me)
2. Hannah is hiding something, or is unsure of her own actions herself.
3. Apparently I must be attractive to some degree, given the circumstances.
4. This is going to be a Win-Lose scenario, I can see that, and
5. I'm getting too emotionally drained from trying to satisfy both girls...
1. She is obviously the jealous type. It is a good thing on the one hand, because it means that she (at least) really likes you, but is not so good at the same time, since it can cause misunderstandings, and bad situations. Just let her know and make her understand, that she is the only one for you. Remind her every day if possible, through sweet talk, and maybe some "I love you"s, if you feel that way.
2. I think the latter is probably true here, although you cant be sure unless you find out more.
3. Really?? You think so?
........
However impossible it might seem to you, I think there is a slight chance that you are attractive as a guy. Lose the low self-esteem and stop laughing about it please.
4. Yes, unfortunately it seems that 1 of the 2 (Mish or Hannah), will be kinda hurt in the end. Win-Lose scenario? I dont think so.
5. You dont have to emotionally satisfy 2 girls. I think most people would pay more attention to her GFs, than their friends. Also, considering that Hannah is NOT your GF, why do you have to "satisfy" her like you say? Being her friend doesnt mean that you have to flirt with her all the time, to make her feel nice. Just saying.
Your thoughts, Gentlemen? Any help would be appreciated, because hopelessness is starting to set it atm.
My thoughts....hmm... 
As hard as I try to keep my personal experiences and opinions out of this, it is kinda impossible.
However, I would say that I will try to be as objective as possible.
1. You dreamed of being with Mish for so long. I would advise you not to ruin this relationship, and maintain it for as long as possible (considering that you do want to be with her ofc).
2. I believe that Mish should know about Hannah's actions, considering that she is your GF, and that Hannah is at least semi-flirting with you. After all, you wouldnt want her to find out the wrong way, and I assure you that it would be a lot worse than you telling her. I understand that you dont want to "rat" on Hannah, after her telling you not to say anything to Mish, but you need to think a little bit more about yourself, about the whole thing. And Hannah doing....whatever it is she's doing, affects both you and your relationship with Mish.
3. I cant know better than you the whole situation, but only you can tell if this is going to turn ugly or not. If Mish finds out, and goes all like "You f*^%ing whore, leave Koda alone!!! DIE!!!" remains to be seen, and you should know if Mish would take it really bad, because more factors come into play here, like Mish's relationship with Hannah, your relationship with her, etc, but the thing is, that you NEED to "clear your nest" here, be honest with both Mish and Hannah, and generally avoid future incoming fire.
Worst case scenario (if you do that), is that Mish and Hannah never speak to each other ever again, you lose Hannah as a friend, and keep your GF (Mish). You definitely do not want to lose them both.
I know, I was being a little extreme here, but I'm just saying 
4. I understand that you are trying to be careful, not make any mistakes because the situation is delicate, but do not take too much damn time trying to figure out what's going on. Time is working against you atm.
I dont think there's a way to be 100% sure about Hannah's feelings towards you. Even she herself might not be sure. Or she is just lying. Its either one or the other. (Although I believe she is unsure, but please dont take my personal opinion into account.)
5. I think its safe to say, that the best play would be to take what Hannah said (she sees you more as a brother...) for granted, tell Mishayla everything, let her know that you only have eyes for her, that Hannah and you are just friends, and try to make it go as smooth as possible. Calm both of them down, with some of your diplomatic tricks (you must have some), but do keep in mind that trying to maintain both of your relationships (Mish and Hannah), might be a little risky, to say the least. You might want to try to give more attention to Mish, and make your relationship with her your #1 priority (protecting it), because you definitely do NOT want everything to do down with a big bang.
The truth shall set you free. After all, you are being the nice guy here, and you havent done anything wrong 
Good luck.
"Human beings are a disease, and we are the cure"