Chinook are less affected by low thiamine concentrations than the other salmonids. Several research studies in the mid-2000s by USGS and Michigan State concluded that chinooks can effectively reproduce with much lower levels of thiamine than coho, steelhead, or lake trout, because they have a lower metabolic requirement than other salmonid species. Here's one of the studies if you care to read it
www.canr.msu.edu/qfc/publications/pdf-pu...almon_Honeyfield.pdf
Chinook thiamine concentration not only varies over time and size of fish, but can also vary between individuals in any given year. So even if many fish have low thiamine concentrations and experience fry mortality, there are still enough fish that have acceptable levels of thiamine and those fry survive. There is likely lots of compensatory mortality in chinook fry - there are far more fry produced than can survive, given available resources. So if lots of them die from early mortality syndrome (caused by low thiamine), the remaining fry can survive at higher rates, due to more available resources.
Studies of the total number of wild fish in Lake Michigan have been ongoing for the better part of 2 decades now. That's why there have been periodic stocking cuts, as the proportion of wild fish increased, both due to increasing reproduction in LM watershed, and after the collapse of Lake Huron, the migration of fish from LH to LM
As for keeping track of where the salmon come from, it's not exactly a simple process. There have been plenty of studies and observations of where chinook natural reproduction is happening. It's not exactly a secret that rivers like the PM, Betsie, Little and Big Manistee, Muskegon churn out tons of wild chinooks. But it has been difficult to quantity the extent lakewide contributed by each river in the LM watershed (and for that matter, Lake Huron).
First, you need to have every single stocked fish be marked. Otherwise you can't 100% reliably tell which is a wild fish. Then, obviously, you need some way of knowing where each of the adult fish came from. You can't exactly interrogate them to find out where they were born. We now have the marking part of the equation, since all the stocked chinooks have been fin-clipped since 2011.
Now, thanks to advances in technology have come a long way, it has become possible to determine the natal origin of adult fish. Basically, you remove the otolith from the adult fish, use a laser to vaporize the otolith core (which was formed in the natal river) and analyze the ratio of elements like Barium, Strontium, and Magnesium. Then you have to have water samples of all the different rivers to match up the chemical signature.
With the arrival of the Great Lakes Mass Marking Program and developments of the otolith microchemistry technique, there is an ongoing study to determine where wild chinook salmon are coming from, and the relative importance of each watershed. There's also a similar study in progress for steelhead