Just thought of this and want to throw it out there, what if you made 6 email templates? You could have a list of email templates to pick from based on how many stories you plan on including in this current issue titled something like 2 Story Template, 3 Story Template etc.
It might be a bit of work up front, but if you usually retain the same design elements on every 3 story template for example, it might be worth cranking these 6 out and then never worrying about editng the template when you change up the number of stories from week to week.
Hope this helps!