I don't think it's bad to indicate where they diverge (but it would be more readable to reference the commit by tag, now you've imported them).
My main concern (sorry if I didn't read it carefully enough and misunderstood) was that your original approach seemed to me to be saying that there would be files in your distro that had portions under one license but subsequent changes under another. I think attempting to apply licenses to an individual file at the commit level is problematic - hence my advice to just accept that modified files are derivative works and will have to be licensed in their entirety under the GNU Affero GPL.
You read me correctly but assumed too much. I wanted to have a record in the license file of when the code started to diverge, since I'll be changing code and licenses in a lot of original files. I've amended that by tag in LICENSE.
The releases is really easy to use. Click on the Releases tab in the github repo and then click on the tag (the name of the tag is a link) you want (in this case 0.93.3). Then click the button to edit the tag and drag and drop the binaries into the box where it says the binaries are. If you want to add a message that goes with the release, type it into the textbox. When you are done click publish release.
Done. Was a lot easier than expected =)