With my experiences fish bite great in the rain, as long as the river level is not on the rise. I think they feel more secure, rain breaks up the water surface and provides a sort of screen. Fishing should turn on big time this weekend, I imagine the Alsea will be a madhouse on Friday! Get there early or for the afternoon bite when a lot of people have left already.
Fish are on the move as soon as the water starts rising, they usually just don't bite. They move less the more the water drops to a low level, but there will be plenty moving until the water clears. At this point in the run there will be fish all throughout the system all the way to the hatchery. Fresh fish might be lower down, but they come up quick. Clemens is a great place to start, if it was me i'd spend the day there and hike around looking for holes. Good luck!