Success with patching Email::Stuff! I saw that it was a part of the Perl Email Project. I got in touch with them about the Email::Stuff bug on their mailing list then followed up on IRC (irc.perl.org #email).
Ricardo SIGNES was good enough to help me investigate if this was an issue with Email::Stuff or one of the underlying Email::modules. He confirmed this was a stuff issue, and also pointed out a couple of other bugs.
I offered to supply patches to fix all these bugs. RJBS pulled Email::Stuff into github and gave me a fork to work on (which for me also meant getting a github account and learning the basics of git). A few hours later I had a fully working fork fixing the header loss issue, unused clone issue, and also multipart/alternative issue. I went further to write unit tests to check that these were working properly and ensure they continued to do so in the future. I also updated the docs a little, although I should probably have documented the new conforming functionality a bit more.
With the minor patch I submitted to Params::Util getting applied but giving me no mention in the changelog. This time I was very chuffed to see my name appear in the credits :)
Patched Email::Stuff 2.07 now on cpan ;)
Clone issue fixed, RT BUG fixed and other problems Ricardo found all fixed.