Did you verify that each HTTPS URL that you produced actually works?
Also, I would prefer to leave "upstream" text unchanged. This includes the comments in Doxyfile.in (which is auto-generated boilerplate from Doxygen) and license text in LICENSE. (Some licenses arguably require verbatim reproduction of the license text, and it's unclear to me whether changing http:// to https:// would be allowed. We could check whether the upstream projects have updated the URLs in their license text, I guess.)