There are some very common branding and UI scripts that a lot of institutions run that will need to be rewritten with the change of UI. Most of these are pretty basic changes.
One in particular:
A lot of schools have added extra pull down menus to the top navigation menu. Our institution added "Library" and "Support" here. We will need to move these to the left side navigation replacing the with icons.
I know we got our code from our implementation manager from Instructure... the nice thing about this is that most institutions had similar code. I wonder if there will be any sample code for this that we could base our implementation on.