First of all, no long distance relationship will work AT ALL if one or both parties lacks confidence or trust. You said it is hard on you because you are a physically-oriented person. Maybe if you have expressed this concern to her a lot, she may assume that you need SOMEONE near you (and not just her) and you are making her feel self conscious? Also, maybe she hasn't answered because she is extremely busy (someone said dorm up ahead, if she is a college student she is probably busy starting school soon?)
Becoming paranoid is not going to make the situation any better, in fact it will raise tensions and may cause an argument. I know it's hard to be out of contact with someone you love. My friend's boyfriend studied abroad in Japan for a year (and she had been dating him for 6 years beforehand!) and it was hard on both of them but you need to stay composed and confident.
Communication will be difficult and frustrating at times, my friends and I often times struggle about talking about complex topics. Are you also trying to learn Japanese? It may be stressful on her if you aren't, because it's like expecting her to carry on all of the conversations in a language she isn't 100% confident in speaking.
I feel like relationships that have distance work a lot better when the people in them have some past foundation to build trust off of. Three months is not a long time to build something like that, but if you stay confident and meet her halfway with the language struggles, I'm sure it can work out until you are able to see her permanently.