Hi Rick,
I think it might help simply to look at the design evolution of any given hole between 1912 and the time it was "finished", which as Tom Paul mentions was over a lengthy period up til the early 30s. If there are specific holes that you are wondering about, perhaps we can discuss about any or all you have questions about, or is your question more general in nature, as in trying to determine whether what's there today is primarily Flynn, Wilson, or any others?
Personally, I was surprised a few years back to see early drawings of the course by 1916 that show most of the holes pretty close to today's, and certainly by 1924 the course was about 80-90% or so like today's course. Since Wilson died in early 1925, it can probably be fairly said that any of the changes done for the 1930 US Amateur were likely Flynn's sole idea, but before then it seems to have been a work in progress, with mostly Wilson at the helm.
Joe Bausch recently came across a news article talking about the changes done for the 1924 US Am, which led to the creation of today's holes 10, 11, 12, & 13, and the article was pretty speciific that Hugh Wilson was the guy who spearheaded and oversaw this work, although it also made very clear that Wilson was a very humble man who preferred to stay out of the limelight and work in the shadows. I'm quite sure he would have been perfectly happy if others had been given credit, and seemed the type who would also have minimized his own role to give others credit if they helped.
Of course, there is little doubt that Flynn was a valuable and instrumental part of the course that was created at Merion East, as he was almost there since the beginning, and early news accounts talk about his professionalism, his knowledge of agronomy, his business sense and frugality, and others mention his architectural acumen. As Tom mentioned, Wayne's the expert with the details, but I think that's a fairly accurate overall assessment.