-- Last Updated: Jul-28-12 1:28 PM EST --
You might want to check out availability of rental cars in Emmonak before you make any further plans. Which highway might you be driving on to leave from there? A quick look at google maps will tell the story.
People who have done this trip have in the past either abandoned their boats, or if they are small enough, they strap them to the exterior of a bush plane to fly someplace where there actually is highway access to the rest of the world.
The last downstream road access in Alaska is at Yukon River Camp on the Dalton Highway, 160 miles north of Fairbanks, which is some 900+ miles upstream from Emmonak. The Yukon River flows 4-6+ miles per hour through much of its 2000+ mile length, perhaps a bit less (but not much less) as it nears the sea. Paddling any distance at all upstream is quite a hefty workout.
Here are a couple of web sites you might want to check out for some further hints:
If you have any specific questions, feel free to ask, or to google. Help is available for you to do your homework and to make informed decisions on if you really want to do this.