OP: so I actually filed as a independent on my tax returns for the first time this year and could answer a few of your questions but I'm not an MD/PhD student:
1) You should confirm that you'll lose your dental benefit from your parents if you file as an independent. Many states have laws that allow children to stay on their parents' healthcare plans regardless of dependency status.
2) Yes there are definite benefits to being independent. The IRS considers you a de facto (and de jure) head of household if you file as an independent and thus you automatically qualify for a large deduction and exemption that makes approx the first 8-9K of your income non-taxable (so you can feed, clothe, and shelter yourself). If you are a dependent, then it is assumed that someone else pays for your basic necessities and they then get an extra exemption and other deductions instead of you.
3) No clue about MD financial aid, but I would check to make sure that your parent's income isn't considered on the FAFSA regardless of your dependency status.
4) Stipends unless you use it for education expenses like books, tuition, etc are usually taxable income. However, your dependency status actually doesn't directly affect your tax bracket.
If you earn enough such that you have to file a separate tax return (regardless if whether it is as a dependent or independent), your income will be taxed according to the bracket that it alone falls into. The threshold for needing to file I believe is somewhere around $1000 a year. In that case, it is not added to your parents' income because it is on a separate return. The main difference is that, as a dependent, you get fewer deductions and exemptions and thus more of your income is taxable.
5) AFAIK, federal grants are generally taxable. How the grants are considered by the IRS depends on who hands you the money basically. If the grant is administered by a school which pays you a stipend, then it might be as earned income (W-2), a grant (1099), misc income (1099MISC), or even self-reported. If the federal govt pays you directly (ie you get paid by the US Treasury biweekly/monthly/whatever), then you get a 1099-G (for gubmint payment!) and it is still usually taxable. The only exceptions are probably for stuff like tuition, books, etc.
Overall, I would delay filing as an independent until after college because of certain rules pertaining to claiming tax credits for tuition and other educational expenses. The reason is that if your parents pay for at least part of your tuition, then they can claim deductions or tax credits from that if they claim you as a dependent. However, if you file as an independent, then you will usually need to claim those deductions or credits yourself. The problem lies in the fact that many students do not make enough income such that they can claim all of that deduction/credit and at least part of some of those deductions/credits are not refundable.
In more concrete terms:
Say you can claim $2000 of credits from paying your tuition. If you are a dependent, then your parents can claim that and reduce their taxes by $2K. But if you file as an independent, then chances are, as a student, you don't actually need to pay $2000 in taxes (which equals about $20K of income assuming a 10% tax rate). Assuming you pay something like $500 in taxes as a student (basically you work part time in school), you then have a balance of -$1500. Since students below 24 (I believe) cannot usually get the difference refunded, you basically lose any negative balance you had and thus you'll end up losing free money because you don't earn enough income to claim all the tax breaks for which you are eligible.
So I would definitely talk with your parents and figure out exactly how much you expect to earn and how much credits/deductions you expect to claim and run your taxes both ways to figure out which one is a better deal.
