You're not going to get scolded - it's a good question.
Academic EM is very different from academic medicine in other fields. Due to the youth of our specialty, the more "conventional" research-heavy medical centers aren't the hotbeds that you might think that they are. MGH/BWH, JHU, Duke (my home school), UCSF, Wash U, etc... were all forced to develop EM departments late in the game due to the strength of either Medicine, Surgery, or both. These "mainstream" Departments wanted to hold on (understandably, since it's a fertile training ground) to their control of the ED. That's why Duke's program is only three years old and UCSF still hasn't managed to start one up (although it's in the works). These newer programs (all mostly Divisions of Medicine or Surgery rather than independant Departments) are all going to do exceptionally well, but they haven't been able to focus as much on research since they've had to deal with more startup issues (funding, recruitment, reputation-building, etc...)
More and more programs in EM are getting into research and you can, honestly, go into most any program and do top-quality work. If you're really interested, your best bet is to read the top EM journals and look at the SAEM and ACEP presentation schedules and see for yourself where the kind of research that you want to do is being done.
IMHO, the top research programs are still the juggernauts that have always been there: Cinci, Denver, Pitt, OHSU, Highland (esp. for a community ED), etc... they just have the support networks in place to make it easy to do the work. Again though - ANY program is going to be able to help you do the work.
As for Board scores, etc... read through some of the FAQs (Yay Quinn!!) and older threads. I think the general consensus you'll get is to apply everywhere you want to go, regardless of your scores. It's a crapshoot anyway so why not pay the extra seven bucks per application?