On the shorter side there is the "South ForK" of the Snake. Or maybe the Upper Colorado. You could spend 3-4 days fishing the Green below Flaming Gorge, it has a few smaller rapids and great campsites.
Not many options comparable to offerings of the Middle Fork that I am aware of that meet the stated qualifications. You might be able to pull a midweek Rogue for that time of the year.
On the shorter side there is the "South ForK" of the Snake. Or maybe the Upper Colorado. You could spend 3-4 days fishing the Green below Flaming Gorge, it has a few smaller rapids and great campsites.
These would be my two suggestions also. Both offer great fly fishing, no permit, and good camping. No real whitewater, but very nice floating & scenery. You could do 2-3 days on each & combine them with a short travel day in between.
KJ
Deschutes below Lake Billy Chinook actually offers two multi-day runs. If you do both runs, total river miles add up to just over 100 miles. I've never fished on it but a friend of mine guided on it for years and says the fishing's great.
There is always the Lower Klamath as well and it is only 6-7 hours from the bay area. If you head all the way up to Oregon the Deschutes runs nicely that time of year. The Grande Ronde is low, but you can still get a boat down it. The Umpqua has lots of multiday flatwater stretches as well. I know people who have floated them in a canoe.
deschutes can be good that time of year but heat during the day means fishing is early or late, Grande Ronde is floatable, but skiiiny that time of year if you go light and float the lower river to Hellar Bar the small mouth fishing can be totally INSANE! I have done a 90 mile canoe trip on the Umpqua, small mouth fishing is way better on the lower GR these days (seriously!). Rogue could also yield good summer steelheading and half pounders. Its the closest and probably your best option.
The fishing for the Rogue starts getting good right about that time, Fall run for Salmon and Steelhead.
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