First of all, thanks for the great feedback.
I was thinking of doing research, not necessarily a formal fellowship program. I know the ones I listed require you to apply months in advance, but in the short time I have, I could find a spot in someones lab and hopefully be able to gain something useful out of that (ie. publication or a good reference). As far as getting excused from the dean, that won't be a problem. I actually am interested in doing research, not just to strengthen my application, I just haven't had the time for it in the last couple years. But at the same time, I have to be realistic and not get involved in something that isn't going anywhere. I want that year to be useful. The other option of course is, like you said, doing research 3rd-4th year but I am guessing you want that time to prepare for the match (eg. the SF match which is earlier) and make use of your electives?
First I would make the decision whether yuo want to take a research year or not. That heavily depends on whay tou think it will get you - be it research training, pubs, connections, a beefier CV for ERAS.
I am of the opnion that only the former should be your reason for taking a year off. Step I and clinical grades are the prime determinants of what residencies you can apply for, and no amount of research will outweigh a poor Step or clinical. If you don't believe me, look at the thread entitled "You know what? Nevermind" in the MD/PhD forum.
Heck, when I was at the NIH, one of my interviewers was a surgeon in specialty X, and he had a med student taking a year off in his lab. The doc tells me this student wants to go into specialty X more than anything, but she likely won't Match because she doesn't have the Step score for it, despite her research work.
Another anectdote - a buddy of mine spends every weekend and free minute over the last 3 years doing research with famous professor in surgical specialty Y. My friend is a smart, hard-working guy who wants nothing more than to be in specialty Y. The famous professor moved away, and now that connection is essentially gone.
So that's why I say that it's not worth it to do a research year for anything other than research training. So if you are interested for that reason, then wait a year. Take a year off after MS3. You'll be surprised at the changes in your confidence with clinical medicine and working with patients. You will be much more useful to any PI because you'll have a better understanding of the constraints of clinical medicine. And you'll be able to apply for those competitive fellowships and get a really good experience.
But at this point, I say focus on Step 1, as that is the next best thing you can improve and thereby enhance your chances/oppoertunities down the line. After that, if you really want the research, in your situation it might be best to wait. Something to consider.