A few points, from someone who lives very close to this site and who has fished it regularly since 1987.
Look at the actual numbers of trout (diagram 2). The numbers are nearly identical in 2007 and 2008.
They only sampled 500 feet, slightly less than 1/10 mile. In most surveys, they survey around 300 meters, or 984 feet. The habitat has been significantly changed over about 1 mile of the stream. Sampling 1/10 mile doesn't tell you much.
They sampled the "flats" behind the dam, which was the poorest habitat area in the stretch influenced by the dam. They did not survey the plunge pools below the dam, or the deep pool at the bend upstream near the gas station. These were the two areas with prime holding water in the stretch affected by the dam removal. These areas held very large numbers of fish, including some larger ones, and these were the two areas most popular with fishermen.
The plunge pools below the dam were eliminated. The bend pools are still there but greatly diminished. It used to be about 5 feet deep there at the deepest point, now it is about 2 feet deep at the deepest point. The pools are also greatly reduced in area, and the gradient is much swifter. What were formerly pools at the bend are becoming more like "pocketwater" as the gradient has increased through headcutting (nick-point migration) because of the removal of grade control.
The habitat structures they have planned for this summer may improve the situation somewhat. Lets hope so. Right now the stretch is mainly steep, swift pocket water, without significant pool habitat.
In the introduction it says that the dam impacted water temperatures, but no data is given. There have been a lot of press releases, articles etc. that have claimed temperature impacts from the dam, but no water temp data has ever been given. If they have the data, they should publish it. If not, they shouldn't make that claim.