if I could only find out which 2 files Google is NOT indexing
What I did was to use site:domainname.com as my Google query, then I manually copied each returned address into a text file, sorted them, and compared to my own list. After doing all that (it was a considerably smaller site than yours!), then I went into GWT and did a Fetch as Googlebot for each of the missing URLs. That process just took place in the past few days and so far, nothing has changed so I cannot say definitely that the problem is solved.