That should be fine. I'll update the OP to point to your commit with the version string fix.
I didn't even try to commit the changes I made due to the massive package renaming that had to be done first in order to publish. Thankfully, I came up with a single command-line call that turns every instance of "mupen64plusae" into "mupen64plus" recursively. Going from "mupen64plusae" to "mupen64plus.free" or "mupen64plus_free" depending on the context will be a bit trickier. I'm going to see if I can write a semi-intelligent script to do the work for me.
Getting an update published to Trev's branch is not currently possible, due to his digital signature being on my computer in storage (he's not a developer himself, so I was building and signing the app for him to publish on his account) I should be moving into our new home in a week or two though, so when I do, I can have Trev re-publish for a few weeks with an updated "1.9.3" version with a popup message like you said. Hell, we could even publish 2.x with a popup, for that matter (although not upgrading might entice folks to switch sooner

) In the mean time, I think it will be best to unpublish his branch until we are able to push the message out to folks, just to avoid confusion.