I would love to see how you integrated common core into your ePortfolio template. Can you share the original? Is it possible the pages were made into templates individually along with the whole site in the original? Can you check the pages in the original and untemplate it or start fresh, perhaps using the templates to create a new site that works as expected?
I'm not sure how many students you are working with, but if it's a lot I, I have a possible solution that might help. I created some scripts because I was not allowed to give students the ability to create sites but we wanted them to use Sites for ePortfolios. It's also been used to push out copies of a site for teacher sites. If you're not dealing with many students then it might just be easier to continue on the path you're already on.
Yesterday, I was deploying ePortfolios to our students (Kindergarten through 9th grade) from a site that was created by our portfolio committee. The trick is you need an account with some admin privileges or help from your Google Apps administrator to run these scripts. You might want to tweak some variables in the script so you have to be okay with looking through some code. When I first made the code it was pretty basic and just cranked out enough for our pilot last year. Since I was working with many more students yesterday, I decided to refine the code making it a bit more complicated but much more user friendly. I added some error handling and many more comments throughout the code. Eventually, I might make a wizard and deploy the script so folks can install it, but for now it's a manual process to get it setup. If you're interested here's a basic presentation which goes over the setup and the code you can cut and paste:
Implementing ePortfolios with Google Apps