You can combine protected files in a portfolio.
I am using Acrobat XI (11.0.20). Portfolio doesn't seem to be an option?
Looking at the Portfolio on this website, I do not see how it applies.
I need to be able to protect the individual PDF's from alteration (other than filling out fields and signing), but allow the end user the ability to combine multiple protected PDF files into one protected "project" pdf.
That's not possible, unless you use a Portfolio, as was mentioned.
In Acrobat XI you can do it via File - Create - PDF Portfolio. Then select your files and merge them.