Your intended route most/part of it, has been covered in numerous trip reports here. Take the time and peruse the trip report forums. I'll bet you will find everything your looking for, or at least narrow your question's list.

3 weeks is plenty of time do do it right. Since it's your first Q trip, I'd suggest taking the time too smell the roses 8-)

You find a nice site, has day trip/base camp possibilities, take it and enjoy the moment. You'll run across so many possible "distractions" along the way, that you'll soon realize you can't see everything in 3 weeks, with a route like yours.

Good advice that time of year, is travel early, get off the BIG water before afternoon winds pick-up. Go with the flow. Storms can pop-up in an instant, I'd have a tarp up first thing in camp. I'd also keep canoes/gear secured and organized, unless you want too chase them down :-[

I'd go over the PCD, and mark the obvious campsites along your chosen route on your trip map. Don't worry too much about the "ratings", there very subjective any ways.  Knowing the locations and having options is the better way too go in my book.

Take plenty of pictures, keep a journal, and submit a trip report when you get back ;)  Old routes take on a new perspective thru fresh eye's ;D

Oh, and being a rookie fisherman, I'd be willing to bet you do as well as anyone in that department. Just remember to keep the rod tip up, a tight line, and don't "lip grab" the Waldos or NP :'(