Though I'd expect you'll get a hard time from some who respond, I'll try to answer your question(s) seriously.
Ivy coaches are aware that "things happen" during high school, and your 4:25 as a soph will tell them that you have some potential. You're right: a big song and dance about how things went for you as a junior will not help! If you have to say *anything* about it, keep it to "tough year--got sick" or something similar. Some further notes:
--As a guy, you can get cut some slack for a bad junior year (though you'll have to "redeem" yourself with a very good cross season); a girl in a similar situation would be likely to get written off ("Oh, she must have matured physically").
--Even running 4:25 as a soph doesn't really separate you from a lot of other guys. Yes, 4:17 or so as a junior would have helped, but might not have put you at or near the top of some Ivy coaches' lists.
--If your grades (and class rank/test scores?--you didn't mention those) are truly just "pretty good," they would only be good enough if you were at, or approaching, a top national HS level--at least for admission at Harvard, and likely at Penn. A coach would have to "burn" one of his/her very few "big breaks from Admissions" to get someone with such academic stats into school.
Yale is in a different situation, as I understand it: athletically, they might have more use for a 4:25-as-a-soph guy; but they seem to get fewer admission breaks, too. I believe other Ivies (e.g. Cornell) *might* be a little more accommodating.
[This assumes that your grades/tests/rank were *actually* "pretty good," and that you weren't just being extremely modest.
[It also assumes that your ethnicity is some flavor of European or Asian. An African/Latin American background would be a whole different ballgame.]
--Whether for the Ivies or for a lot of other quality academic colleges, a good summer and fall of running will help a lot, as you've already figured out. Try the Summer of Malmo (use the Search function or Google, if you're not familiar with it), but paying *particular* attention to keeping well within yourself when doing the faster work. Summer running should be fun, a chance to get some good miles in and train with others, not a grim-death affair.
--I'm guessing you have a few weeks of school left this semester. Study like a madman, work hard on your assignments, and get *really* good grades for this semester--they'll help with admissions anywhere. And if your standardized-test scores so far have been anything less than stellar, schedule some test prep before your next round of those exams. If you have the discipline, use prep books on your own (you can probably get some from the public library); otherwise, consider a test-prep course.
[Full disclosure: after my track-coaching career, I worked for Kaplan for several years.]
--If you haven't already, get in touch *now* with the coaches of the top-academic colleges you're interested in. Don't wait until you have a great xc season! As I say, some will be interested based just on that soph 4:25; and the degree to which coaches respond to your contacting them now, may give you a clue to how interested they are in you.
--In any case, DON'T "give up." For the next twelve months study, run, and prep for tests as though you expected to be admitted everywhere. In 20+ years of college coaching, including in the Ivy League, I've seen too many admissions surprises (both good and bad) to be able to predict anyone's admission chances very accurately.
Sorry for the long post. I don't have time to shorten it.
Good luck. Please bump this thread occasionally and keep us posted on developments.