It's worth going (IMHO) despite the crowds, and the bike route makes for good riding in its own right....subject to up-to-date information about the roads, which suffered a lot during the January rains. Crowds should be less than normal, given the limited train access at the moment. I presume the OP knows he's not riding to Aguas Calientes, right? Unless there's a highway that's been kept secret all these years.
Information on trekking options, costs, and the various silly rules is all over the Lonely Planet Thorntree, South America branch. Start with the sticky about the floods posted on the first page, then do a search for more basics.
Hope that helps.