I got into a number of top-tier programs with the goal of going into a research career in linguistics, and didn't apply to any non-top-tier programs, for reasons I mention below. So this might be a little too cautious-sounding for people; take this with a grain of salt.
0. Do linguistics. Research is nice, having a cohesive plan for how to expand it in grad school is great. I got involved with several grad-level projects in the summer before my fall app cycle, so it's not too late to start.
1. One thing I want to emphasize, regarding your compiling of the lists of schools to apply to, is to seriously consider what the reality of doing a linguistics PhD program is if you haven't yet. Majoring in linguistics as an undergrad (with no double-majors or anything else on the side) is pretty bad for job prospects; a PhD is worse since you're losing 5 years of potential earnings, and if you think grad programs are competitive, consider how stupidly bad the job market for linguistics is after you finish, regardless of what school you come out of. For example, two of my advisors actually recommended against applying to a particular UC school because they were "Tier 2" and the job prospects aren't worth the time and effort. Note that this school, and other "Tier 2" schools, are highly competitive and definitely worth going to if for other fields like the hard sciences.
Now the school you go to obviously isn't everything in terms of job competitiveness and great work is coming out of less prestigious departments, but there's no question that you would have an easier time after grad school in certain other fields.
Jobs are definitely one reason why I didn't consider ling grad programs until near the very end of my undergraduate career. It wasn't until the combination of the interesting courses I took at the LSA Institute, finding enjoyment in working on a senior thesis, and professors telling me that I'd probably get into some top-tier school that I finally took the plunge. (This meant rushing to work on the apps and study/take the GRE, all the while working on coursework and a thesis, so my second tip: Start sooner than I did.)
Aside from the jobs, regardless of whether you are willing to look at non-top-tier schools:
2. (Ab)use your professors. It's out of your control at this point whether your school has professors who are active in the field and are aware of the reputation of/your compatibility with other graduate programs. But if you do have people like this, it's absolutely in your best interest to go up to them and ask for help with the application process beyond just letters of rec -- they will know which schools are at the top, which are slightly lower, and so on. Talking to professors goes double if you're actually in a PhD-granting program, because that means they're used to reading personal statements! Have them proofread it for you (but make sure to get multiple opinions if you do). Ideally, professors in your department should know you well enough from the courses/projects you've done with them to give you good suggestions for programs and write you a good letter.
A caveat: If these professors are older, they may be basing their opinion on old reputations based on dead/retired colleagues. Linguistics departments are changing rapidly, some faster than others. As the other posters have said, use your best judgment.
3. Be bold. You have to be bold to survive in academia anyway, so why not start in your application? Apply to good schools, for reasons mentioned above, and write a good personal statement that describes just how awesome you are and why these places should pay you to go there. It's difficult to avoid sounding too arrogant or pompous, but confidence is good.
4. Apply for external fellowships.