Hmmm didn't get notified of any extra posts to this thread so I missed all of this!
I'll just make it clear for anyone still having issues...
Adding each update consecutively using DISM to your image should install Windows 7 to a point where it has a majoirty of the updates and the updater should be in working order to pull the last few remaining updates (under 100 of them).
The order I added the updates to my install.wim was this:
Service Pack 1 - I had to
follow this guide to manually add SP1 to my Enterprise install.wim file since an official release does not exist.
KB3020369 April 2015 Service Stack Update
KB3125574 Convenience Roll Up
KB3161608 June 2016 Roll Up
KB3164033 June 14 2016 Security Update
KB3172605 July 2016 Roll Up
KB3179573 August 2016 Roll Up
Once I had these added, I committed my changes with the unmount command and simply put the modified install.wim in the sources folder on my bootable flash drive that had an unmodified version of Windows 7. Then installing Windows 7 worked flawlessly and the updates I had injected were also visible as installed updates in "Installed Updates".
After verifying that I opened Windows Update and was able to successfully check for updates and execute them. There were 71 important updates total left.
To save myself time and bandwidth at work I am going to be adding the Windows Readiness Tool since that is another large update. IE 11 seems like another good one to integrate as it is also quite large. After that everything else is sub 50MB per update - most of them being security updates that are merely KBs large. They install quickly and require minimal reboots. I went from a "fresh" install of Win 7 Ent to a completely updated one within 30 minutes and only one shutdown and one restart.
Edit: I've never seen that May Roll Up until your post and I searched and searched for it - no idea how I missed it. I might as well add that one too, but it doesn't appear have a crucial effect on Enterprise to function properly.