An update to this old thread:
First of all, I was never really able to follow through on any of these ideas. I moved out of the area for work and simply didn't have the time. I don't know if I ever will, but I do truly appreciate those of you who read this before and offered support.
I was home visiting family this past weekend and was able to sneak out to this creek for about 2 hrs on Easter Sunday (yesterday). The physical habitat in the stream is still in very rough shape, but I am happy to report the strong year class I observed at the time of the OP has survived well and seemingly adjusted to the shallower pools. I caught and saw a lot of 4-7" brookies, most appeared well fed. Food has never been the issue here though.
Although the stream is almost unrecognizable in some parts, I am very impressed at the resiliency of these fish. Obviously, the major floods from a few years ago took a big initial hit, but much of the stream seems to be recovering. The upper part was only slightly improved in terms of numbers of fish, but the lower part was looking good with multiple fish in each pool. That may change this summer, we are likely heading for a hot and dry summer which will make things a bit cramped for these trout, but there are enough now that the population should be alright in the end.
The habitat is still a mess overall. Essentially, over the last 2-3 years, an extra half foot or more of sediment has been dumped in nearly the entire length of the stream, especially below one tributary. There are a few improved areas however, with new logjams creating a couple plunge pools. It may be just enough to offset the complete loss of other pools to sedimentation. The problem in the recent past has been that these log jams get blown out before the plunge pools fully form. Given another year without another blowout flood, things could get pretty good once again. Time will tell...I am hopeful.
Yesterday I realized that I really should have been paying attention to the one problem tributary all along. It was obvious that this trib is just dumping an incredible amount of silt and gravel into the stream. It drains a very steep valley along an old sewer line, then blows over the gravel road, taking chunks of roadway with it, and that all ends up in the main stream. If that could be controlled, it would help tremendously. The rest of the watershed, while it is "flashy", probably isn't about to cause a catastrophic sediment dump like this one tributary seems to be attempting to do.
May have a few pics later