First, don't stress. There's ZERO point in stressing out about anything. You'll make it into schools (even if they're not the best ones ever), you'll get a great education (it's more what you make of it than what they give you, no matter where you go), you'll make great friends no matter where you go, and you should enjoy your last year in high school, you'll never get another one.
If you want to go into research, then you're likely looking at grad school too, amirite?
If so, and you're dead set on going to grad school, then worry a bit less about undergrad location. If that's the case, undergrad is really just a primer to get you ready to get into the right grad school, and many undergrad institutions can get you into the grad school you really want. If you're dead set on grad school, then going to the best in-state school is often a great route to go.
As far as getting into undergrad, they say "we look at EVERYTHING" to sound good. When it comes down to it, if they have 10,000 applications, how carefully do you really think they read them? You do need things that are going to stand out, because they do read everything, but not that carefully in my experience. If your measurables are good (I came through after they added 800pts of writing to the SAT, what's your reading/verbal SAT without the writing out of 1600?) and you have things like Eagle Scout, extra curriculars, etc, then honestly you're in about as good a shape as you can be. Concentrate on your essays and making yourself stand out in those. Get people to read them for you, work on them over and over. Don't put essays off to the last minute, they need work and revisions and re-writing. It sounds like you still have time to put together some experiences for those, you're applying next year, right? There is info all over the web about good application essays and what is good for them. In a lot of ways, it's still a crap shoot though.
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On a more personal level, have you visited either of these places? Make sure you do, and make sure that they're really what you want. I visited both over the course of applying for undergrad and grad school, and I realized that I couldn't live in either place. Both great schools, and I know multiple people who have attended or are attending both (especially MIT, I have multiple of each of high school classmates, undergrad classmates, and grad school classmates that did undergrad, grad, or both degrees there), but they're not for everybody no matter how good they are. I also have graduate classes now where I'm orders of magnitude more prepared than my classmates who did their undergrad at MIT, and I went to a public school for undergrad.
The biggest thing is to visit them. They both have totally different feels about them, and neither feels like any other school in the country.
Remember CalTech is a TINY school, even when class is in session it feels like an empty campus, and really does feel how they describe, like a research institution with a tiny university tacked onto it. Pasadena is interesting, but is in the LA metro area, and I found on multiple visits there (and I live a couple hours away from there now) that I didn't want to be so interstate dependent, and you kindof have to be in LA, because it would be tough to get anywhere outside of Pasadena without depending on interstate driving in your car. I believe you can totally do MIT without your own car, but I couldn't imagine doing so at CalTech, although I'm certain there are many people who go there without cars. I found that Pasadena, on the whole, was ok for me, but it wasn't quite enough, and I didn't like a lot of the rest of LA.
MIT is in the great metropolis of Boston, an awesome city by all accounts, but I personally couldn't do it. The vibe of the school is totally right for me for the most part, the geekiest place out there, but I couldn't do the city and the weather, and I found that I wanted to have more fun while in school. My classmates now in grad school with undergrad degrees from MIT tell me that they hate it while they'e doing it, but love it when they're done. I didn't want that, I wanted some fun while in school, so it wasn't the place for me. No doubt, the place is hardcore, and may be right for you, but make sure it is right for you before you commit to it.
Like I said, I decided to go to a public school in-state for undergrad, knowing that I was 90% certain going to grad school anyway. This school was a top-25 level school for the degree I wanted (whereas MIT and CalTech are both top 5). But with a top 25 undergrad degree, I didn't find it difficult at all to get into a top 5 grad school, the exact grad school I wanted to go to (and ranked better than CalTech and MIT both for the field I'm in). Oh, and I graduated from undergrad with a wealth of fun experiences and zero debt thanks to cheap public school.
Any other questions? Did I help any at all?