Hey,
Well, I have some good news for you--they don't care about your high school grades. I dropped out of high school in the U.S. and got my GED. I haven't been asked once where my high school grades are or WHY I dropped out, though every time I submit an application I go to the school so I can explain what the GED is, because they become very confused otherwise. By the time I dropped out I probably had around 1.3gpa or so.
Acceptance for foreigners into Japanese universities GENERALLY relies on 3 things:
(0) EJU scores (All that matters is that you have the minimum required score for each subject, though some universities may consider it more closely. Minimum is usuall 219 for Japanese, though sometimes 280.)
(1) Timed short essay (often 400-800 letters in 60mins, some universities require 1000, 1600 letters)
(2) Interview (sometimes in a group, sometimes individual, they ask you why you want to enter that department of that university, why you came to japan, among other very general questions, they may ask you to explain something scientifically if you're applying to a science department)
Financial capability to pay for university and living expenses in Japan are obvious and go without saying.
In addition, a few rare schools will ask you to submit any standardized test
scores generally required for admission to universities in your home country (SAT, ACT scores for the U.S.). Other schools will require you to take the university's own written exam.
I didn't apply for any national universities, though (the math and science requirements were a little out of reach for me), so I cant advise you too much there. I IMAGINE Tokyo University will pay a little more attention to everything, including grades.
What is it that you want to study in Japan? I, or someone else around here, may be able to recommend some universities noted for that field.
If you're going to apply to universities for 2010 admissions, make sure you take the June (july?) 2009 EJU and the October 2009 EJU. This means I hope you're already fluent in Japanese. If you haven't had many in-depth conversations about the economy in Japanese, and your reading list is shy of a half-a-dozen non-fiction books (in Japanese), you may want to set your aim for coming to a Japanese language school in October 2009, and entering university in April 2011.
Most foreigners who enter Japanese universities (mostly Chinese and Korean) attend a Japanese language school in Japan for 2 years first. If you're already somewhere around JLPT level 2, you can do a 1 year course. If you can do JLPT level 3 or so, you can do a 1.5 year course. (You dont have to actually take the exam, but you have to have that ability. Some language schools may ask you for the JLPT certification if you haven't taken X hours of formal classes--though you could lie and say you took Japanese at your high school and they would never know it, they're not going to call your high school.)
The October route, might be a good option as it would allow you to move out of your parents sooner but avoid the costs associated with doing a semester at uni in the States and getting an apartment and everything there

. (The intially costs getting set up when you come over to Japan are quite high, as I'm sure you've already been told many many times. Reikin, shikikin, hoshonin daikou, adds up fast.)
While I did find that everyone was very welcoming to an American applicant, and I imagine I receive some benefit from being American, interviewers and university staff were all VERY skeptical that I could understand, read and write Japanese. I believe this works against you if you are poor at speaking, but works for you if you can awe them with your articulate Japanese speech. (In other words, if you can speak well, they assume you study hard so you can read kanji as well, if you speak poorly, they assume you probably can't read kanji either).
I wrote a rather large pdf pamphlet on Japanese University entrance exams a while back, I'll have to find where I uploaded it to. If you have any more questions, feel free to ask. My internet access is a little sporadic, but I should be online for a couple days. You can also email me personally, if you like, i.r.cool at gmail dot com.
Hope to see you here someday,
Chris