Here is where I ended the day. I have looked at the source files for version 4 and it looks like this patch should work in version 4, but I have not figured out how to get the right ckeditor.pack file for the current version of ckeditor matched to the source files and compile the patch into ckeditor.
For now, I updated my ckeditor installation to version 184.108.40.206 and I have all the customizations working in that. The awesome css matching I am getting now is much more important than having version 4*.
Until I can figure out and test this in version 4, I'll stick with this.
I'm going to post a zip file of the ckeditor files that I am using for anyone who wants them.