There is an organized SAG ride across Canada every year. Go here: http://www.tourducanada.com/
It is quite expensive and takes a long time but my husband is very interested in it and would like to do this some time when we can afford both the time and the money.
He biked alone from Ottawa to PEI a couple of years ago. It took him about 12 days to get to the coast – about 100 km per day.
There are plenty of people who have done similar things so I am sure you can get lots of advice on the internet.
Some of his pics are at http://www.flickr.com/photos/bikeriders/sets/678890/ although since he went over the 200 photo limit, some of them have been deleted.

I’ve ridden over the continential divide twice in the Canadian Rockies, and over the highest paved road in Canada. It actually is not that hard to do.

But what I’d find the most daunting is what other people have mentioned—going across Saskatchewan and Manitoba, and the western part of Ontario. Man oh man, as much as I generally don’t approve of riding with headphones, I wouldn’t want to do that without an mp3 player and 3000 tunes to listen to.

Canada is a beautiful country and your goal seems to me very do-able.