Just thought I would reply to your post while I had the chance. I have done some preliminary planning of what I want to bring on tour in terms of clothing, and can hopefully help you out. For bottoms, I plan to bring 2 pairs of biking shorts, 1 pair of pants that will be good for biking on colder days, and then I am still deciding between 1 or 2 pairs of pants for campsite/sleeping use. I also have a set of leg warmers, to be worn with biking shorts for warm days and cold mornings that can be easily stripped away or rolled down. There is a great packing list on the Otesha website under clothing, at the bottom (
http://otesha.ca/content/gear-list-0) that I used as my guide for planning and then the question really comes down to how much do you want to carry? And you know your body best and what you might need to bring (ex. fleece bottoms or just shorts for sleeping in).
From my few years of canoe tripping experience, it is also a good idea to set aside a set of clothes (generally pants and a warm shirt) that stay water proofed in your bag until bed time, regardless of how wet you get during the day or if your "day clothes" are still wet in the morning because if they get wet then you are out of luck for the night or for warming up later.
Hopefully this has been helpful.
Michèle