The future brood document is the correct reference, but it is so large (~1200 pages) that unless you have some idea where to look, it is basically useless. I'll attempt to answer some of the questions based on memory.

RunNGun: There used to be coho net pen programs damn near everywhere. The largest ones were in South Sound at South Sound Net Pens (WDFW) and Squaxin Island Net Pens (Squaxin Tribe). Both of these were at the same location next to Squaxin Island. Fox Island (WDFW) also had a very large program, but there were also substantial net pen programs in lakes near the Nisqually River (Sequalitchew Lk.) and in the Puyallup River (Kapowsin Lk.). In addition, just about every marina in S. South (and probably the rest of Puget Sound) had one or two net pens that were cooperatively taken care of by local sports groups. Hood Canal also had a stable program at Port Gamble and the Suquamish Tribe had a large program at Agate Pass. Hood Canal added a net pen program at Quilcene Bay as well. (Elliott Bay coho pens came in some time here, but I'm less certain about their history than further south, so I won't comment about them.)

I did not work for WDFW so I can't say for sure why many of the programs ended. Outsiders were told that it was because of budget cuts and I suspect budget played a big role, but when you use that excuse, you really are just saying that other things were more important. In order to deal with the "budget cuts" and still keep facilities operating, WDFW switched the release program at many of the marine sites to fall Chinook yearlings assuming that since the contribution of FCS yearlings at Percival Cove (Deschutes R.) was high, the net pens contribution would also be high. By switching to Chinook, they also felt that they could simply switch the cost of production to the Puget Sound Recreational Fisheries Enhancement Fund since its legislation called for the release of FCS yearlings to contribute to the winter blackmouth recreational fishery. So, some of the larger programs were switched to Chinook yearlings. There were two major problems...those FCS yearlings were not as easy to rear in salt water as coho yearlings and they did not contribute well to the fishery. That low fishery contribution was also found in freshwater facilities where they started raising the fall Chinook as well. Since there was little effort to actually evaluate the program changes, what really happened was that a bunch of money was wasted to give the impression that they were "producing" when they were really only producing releases and not returns. (Fairly common for many hatchery programs at the time.). The last problem for the FCS yearling net pen releases, came with the listing of Puget Sound Chinook under the ESA. Since all of these fish were released in salt water, there really was not a collection site for the returning adults to swim into, so there was an assumption that they created a higher risk of straying and spawning with natural populations than fish reared and released at a freshwater site with collection facilities. Frankly, from my looks at the CWT information that we finally got, the survivals were so poor that straying wasn't an issue. It just made no sense to release them. [That's my recollection of the evolution of the net pen programs. CM or others here may have additional information.]

stonefish: The Elliott Bay net pen program is confusing. The Future Brood Document says the program uses native Green River coho, the brood origin is "mixed" and the program is integrated. I'm afraid that some of the language used here has gotten pretty loose, so I'm not sure exactly what is going on. If the stock is truly Green River native, I don't think the brood origin should be "mixed." The source of the eggs for the "integrated" program is also unclear. I can only find egg takes from hatchery facilities contributing to the program rather than taking eggs from natural spawners (required to be "integrated" by what it was defined as. Perhaps there has been a change.). If you look at the combined releases of Green River native coho, both from net pens and freshwater facilities, this is huge combined program, and I doubt if there are enough naturally produced coho in the Green River to actually successfully integrate it. The marking is also very strange. The fish released from WDFW facilities seem to be marked. The ones from the net pen are not except for a small group for evaluation. If it were really some sort of highly integrated "recovery" program, that would make sense, but it is not. Good luck figuring anything else out.