You would add it to the email template.
Are you sure they don't show up in Notepad? Usually that is caused again by strange characters added by Word. Since you are sending it to me in pdf format it is kind of comparing apples to oranges and makes it hard to find what the issue is in the format it occurs in.
Maybe if you send the email and then save a copy of the exact text you pasted when you sent the email as well as a copy of the email that was sent, then I could scrutinize what the exact issue is. Looking at word documents to try to find formatting issues that are occurring in other formats is difficult if not impossible.