Wow - for sure we must have attended some of the same classes!
I took some biochem (metabolic 311A and the 300D lab in 98-99) but graduated in Anatomy and Cell Biology. I got an interview the two years I applied to McGill med, but was waitlisted both times (extra annoying since everyone on the list got off the year *before* I applied!!!) In my case I'm pretty sure it was the 3.46 GPA that kept me out.
That's too bad about the AMCAS application - accouting for Cegep really is a pain.
I'm not sure if it was "right" but a representative on the phone told me to just say I had 30 AP credits (equivalent to freshman year of university). If you're interviewed then you should definitely give the schools a copy of your John Abbott transcript to prove you did all the basic science prerequisites. It worked for me, but you should call AMCAS again (especially in Jan-Feb once they're done with this application cycle) to be sure.
btw, I think there was a form on AMCAS for transcript exemptions - did you fill it out properly before they contacted you? If so they really screwed you, sorry.
But definitely don't give up on applying again - you *can* get in, you just need to be extra diligent.
Have the Cegep issue straighted out in time for June, work on the PS and keep adding to your EC's, and definitely do your research to make sure you apply to schools you have the best chance at (as an out-of-state permanent resident). Obviously don't count on the UC's, but you might as well give them a shot anyway - you never know if an adcom might be taken by your personal/cultural history! But the key is to have a good range.
Bonne chance!