Clearly define your relationship with this person prior to moving in with them. Roommates often require a different level of 'friendship', and typically a whole lot more tolerance than the average person has to offer.
Here is what I, a casual observer, take away from your self descriptions in this paragraph. I'm a big guy that doesn't dress very well, nor am I overly invested in my appearance. I strive to be non-chalant about it but on the inside I know it's why most people can't approach me.
Here's the deal, insecurity sucks because the only person that can change it is you. Insecurity is compounded by the fact that people can smell it a mile away, and you are right, it does effect your ability to become close to them.
You can talk at length, in class, about subjects that interest and excite you. Conversations held outside of class there is no focus, no pertinent subject matter, literally no cohesion. I wonder what would happen if you could find people with interests similar to your own, if you would still have problems conversing...
Real world translation: I can justify my 'antics' at a party or some other goings on because everyone else is doing the same thing. You show me the truth in that and prove the lie that it doesn't make me a whore.
She's trying to tell you that she doesn't find you attractive, without getting in to any of the specific reasons. In truth, this is a deficiency on her part, neither having the ability to see the attractive parts of you, nor the balls to tell you straight out. Don't put any stock into what she says, aside from the inferred "I will never sleep with you".
Aside from my previous comments about why you should disregard what the girl said, you can't change who you are. After reading your posts I'm coming away with a feeling of latent insecurity, most likely appearance based, which is almost definitely unfounded. The worst thing anyone ever did to my social life was to convince me that I was somehow not good enough or handsome enough to run with the 'popular' crowds. And what makes it even worse is that particular wound was self inflicted. Once you understand that the problems people have with you are their problems, not yours, you free yourself from all of the wonderful bullshit that accompanies social endeavours. The fact of the matter is that there is only one 'you' in existence. That makes you both the best and worst example of what 'you' can be. If people don't get that, there's nothing you can do about it.
I'm going to give you a powerful and useful mantra, applicable in the following situations:
People don't like the way you look
People don't like the way you talk
People don't like the way you act
People don't like the way you think
The mantra...
Fuck 'em, there's more out there for me to choose from