I think your opening the broodstocking can of worms and I feel your pain concerning the Skagit. Under your scenerio, if I've got it right, you want to capture wild adult chinook for your egg take, incubate the eggs thus eliminating the mortality that normally occurs in the gravel, then releaseing the fry as wild fish. I would think that this would be a good plan and don't feel that the released fish would have time to aquire any of the negative traits that fish reared to smolt in a hatchery would take on. Many programs that utilize remote site incubators are basically doing what you want. One problem on the Skagit with chinook would be legally gathering your adults with all the ESA restrictions on them. Another consideration for any system would be whether the system can support (carrying capacity) all the fry your sending out if your doing a big project. It wouldn't make much sense to put out a ton of fry if there is not enough habitat to support them.

Beezer