I liked the idea of uploading the changes to the core that you've made. You can also clone the Q2A repository to your Github account and then just edit the files online and do a commit after that (I think it happens automatically). Then getting a diff of the changes is super easy.
Specifically answering your question, I've taken the files locally to my installation, asked a question, and then got the email properly formatted. I'm assuming you're talking about the A new question has been asked by... email. It also was received in the appropriate content type: text/html; charset=utf-8
So there is something else going on. Look in your email client a Show original email (or something like that)to see the content of the email you're really receiving. Paste it in your question removing any relevant content. It won't be possible to provide help without that.
- Are you using the WYSIWYG editor? If not which one?
- Are you getting the same results in different email clients? (e.g.: Google, Yahoo, etc)