Primary research of the Lewis and Clark Expedition should start with the Lewis and Clark journals. There are many versions for researchers to choose from, but the Journals of the Lewis and Clark Expedition edited by Gary Moulton and published by the University of Nebraska Press are authoritative and complete. The can be accessed in print, or online at: http://lewisandclarkjournals.unl.edu/.
The Lewis & Clark College Special Collections have other all of the other edited versions of the journals, as well as microfilm images of the original manuscripts.