Melissa,
My initial impression is that your proposed Itinerary is a bit too "ambitious" for a six week trip. Visiting 16 destinations in 42 days is only an average of about 2.6 days in each place (with no allowances for travel times, especially to Greece).
Regarding your numbered questions:
1.) My preference would be to book plane tickets soon. A lot of the charters will be discontinuing Europe service at about that time, so the remaining seats may be more expensive. However, I don't know what flight options are available from your location? Would flying from Calgary be an option? You might check Air Transat to see if that might work.
2.) I always tend to pre-book accommodations, as I don't want to waste valuable travel time looking for something when I arrive in an unfamiliar city. That way I get to choose both the price range of the Hotel as well as which part of the city it's located in.
3.) I'd suggest at least a GoreTex or other waterproof coat as well as a sweater or whatever that you can use for "layering". I've travelled at that time of the year, and the weather has been reasonably good but of course one has to plan for the worst case.
I'm sure the rest of the group will have a few thoughts as well.
Cheers!