June 2010: you submit your AMCAS primary application
Summer 2010: secondary applications sent
Fall 2010: interviews are held
Winter/Spring 2011: acceptances finalized
Fall 2011: start class
Close. Secondaries are sent Summer/Fall. Most schools have a secondary deadline around Nov 1st, but some are later (I've seen December 1st). Obviously, you don't want to wait that long to submit secondaries - you should submit them as soon as you receive them.
Most MD schools do interviews Sept/Oct through Feb/Marchish. Since they do rolling admissions, you're usually better off interviewing early in the year, as a school may have filled all of their spots by December and waitlist people from there on out.
Schools have different timelines on acceptances. OSU typically notifies people within 2 weeks if they have been accepted, rejected or "deferred" (which is basically waitlisted), but some schools can take up to 2 months to notify applicants, especially if you interviewed right before the holidays.
Schools can accept people after deferring or waitlisting them at any time. I was initially waitlisted at one school in January, then offered an acceptance in February. I interviewed at OSU in February, was deferred, and then accepted in May. Schools can accept people off of waitlists up until the day classes start - I've even heard of people being offered spots on the first day of classes because somebody didn't show up the first day.
I assume that if you register for a second MCAT, that your application will be held until the updated score is received.
Maybe, maybe not. Depends on what the first score is.