I believe they headed north, back over the divide (into Montana), then over Lolo Pass, So roughly:
ID28 to Salmon, US93 over Lost Trail Pass, US12 over Lolo.
US12 follows the river, while the expedition stuck to the ridge line to the north. I believe there is a FS road that follows that (Lolo Motor Way).
At present day Lewiston/Clarkston, they took the Snake River to the Columbia to the coast.
US12 west of Lewiston follows the (dry) valley through Pomeroy, which is roughly the return route for L&C (traveling overland instead of the river).
WA state map w/ L&C poi 2004 edition I84, WA14, US30, and WA4 follow the Columbia to the coast. I recall some mention of the expedition at Beacon Rock SP (WA side).
Cape Disappointment SP and Ft Stevens SP are on either side of the Columbia mouth. I believe L&C first saw the ocean from the Washington side, but spent the winter on the Oregon side.