Yep....which brings us full circle to my original question. Not sure why "You should see some of the remaining 15 in Search Console though. Not sure why you aren't seeing as many are older links."
It's frustrating because most sites ranking above me for certain keywords have crappy links and zero edu/gov links. I have to be missing something. I ran all the tools that others have recommended on this thread and, other an missing alt tags, I don't see any issues.
The only thing I can think of that some of these links point to pages that are 301 to new pages. We migrated from ASP classic to .Net so pages had to be renamed but we went through the process of doing the 301 correctly and notifying google via sitemaps.