We left Prudhoe Bay, Alaska in June 2008 and are now in Bolivia - it's been a fantastic ride so far!
Through Canada you have the choice of two routes - the Alaska Highway or the Cassiar Highway. We took the Alaska Highway because all the cyclists we passed told us of more wildlife on that route. I don't know if that changes year to year or not, but we saw lots of bison, big horn sheep, caribou, and bear on the road.
Through the USA, the standard route is the Pacific Coast. If you have never cycled the coast, you really should do that. If you have, choose whichever route you want.
If you do the Pacific Coast, you will head down into Baja California. It's a fabulous ride - one of our favorites ever!
From there you will cross to Mazatlan and head south. Be aware that you'll have a few days of HORRID road - no shoulder and steep drop-off. We've never cycled that part, but have heard from enough people to beleive it...
Central America is pretty straight forward. There are a few options, but you'll talk with plenty of other cyclists by then and will know which route you want to take.
There is no road between Panama and Colombia - you will have to fly or take a boat. I wrote up a series of articles about our boat crossing - starts here:
http://ww.examiner.com/x-6098-Boise-...olombia--Day-0
Don't believe the reports you hear about Colombia - it's a delightful place for cycling! cycling is a major pastime in the country, so you will be treated as a hero for biking through. It's beautiful with wonderful people and delicious food!
Ecuador is incredible - you'llchance upon so many bright, colorful celebrations it'll blow your mind.
You have two choices through Peru - the gorgeous barren coastal desert that is flat but you'll battle headwinds every day or the mountains where you'll have wonderful scenery, but tough, tough climb every day. We did the coast so I can't say much about the mountian route.
I hope that answers some of your questions. Basically - just get on your bike and start riding and you'll figure it all out once you get there.