Lewis & Clark did not have the 1803 Harper's Ferry Rifle as the contract for that rifle was not let until August 1803. By August, Lewis was already on his way to meet up with Clark. Lewis obtained 15 rifles from Harper's in the Spring of 1803.
The weapons obtained were a mix of 1792 contract rifles -- "Pennsylvania-style, single shot, muzzleloading flintlock rifles, with no ornamentation, hand-made by gunsmiths in Pennsylvania. Full stocked, they had an original barrel length of 42 inches. Lewis says that he had the rifles "prepared" for the expedition. No note was made of what was done, but it may have included shortening the long barrels a bit to make them handier in boats, and the rifling may have been refreshed, increasing the original caliber of the contract rifles. The other gun of daily use was what was then called the “Charleville pattern” musket, the standard firearm of US soldiers of the period (all but a few men on the expedition were US Army personnel). It is a 69 caliber smoothbore and is now called the “Model 1795 Springfield” musket."
http://westernexplorers.us/Lewis-and-Clark-Expedition-firearms-summary.html