SF -
I don't know.
The early life history is such that any of a number of factors could be limiting their recruitment success. It is clear that it is more of local effect than a Puget Sound wild problem. The San Juan Island fish seem to be producing good numbers of young fish with the fish in Possession are not; twenty years ago it was the exact opposite with several good years on Possession and poor recruitment up north.
Maybe it would help to have a quick early life history review of ling cod. The fish spawn in the late winter period with the females laying their egg masses in places like rock ledges, crevices, etc.. The number of eggs of the female vary significantly depending on the size of the fish. A 10# fish may have 60,000 eggs while a 30# may have more than 10 times as many. Once the eggs are laid the male take overs the guard duty protecting the egg mass from predators. When the eggs hatch the small fry (as small as 1/4 inch) are pelagic essentially floating with the current feeding on copepods. By mid-summer the lucky fish will have grown to about 3 inches at which point they settle to the bottom. The successful fish land in eel grass or kelp forests and begin behaving like the larger ling eating small bites of the same foods. They grow pretty quickly with the Puget Sound females reaching the legal slot minimum size in 3 or 4 years with the males taking a year or so longer. The females are reaching maturing at about that point the males at 18 inches or age two. The females continue the more rapid grow; growing through the protected slot limit in 5 or 6 years. The males themselves are slower growing rarely exceeding 36 inches in length. It is rare for a ling t make it past its teen years.
Potential mortality could occur to the egg masses. Smaller males may not be able to effect defend the egg mass or predation by seals or other predators of the males could remove the guarding male leaving the egg mass at risk. The hatching fry success may depend on the whims of a number of factors; is their hatching timing in sync with the copepod blooms or other food sources, will the currents carry to the fry to food sources or at the time for settling to the bottom they may not be able to find the needed habitat structure for their survival. Of along the process the small lings are especially vulnerable to predation. We all are familiar with the importance of food availability and timing as we see their effect on the year to year survival of resident coho. And of course there is the very real potential that Puget Sound is becoming a habitat that is toxic to the juvenile lings.
Don't if any of the above helps.
Curt