Batch Split, Rename and Protect PDF Payslip using Automator

I don't see this moving forward past step 1.

The trick is getting the full employee name and ID out of the individual split PDF file. To do that, one must know how that data is arranged on the PDF page. For example:

Employee Name: Jon Jones Martian  Employee ID: 12345



or

Employee Name: Jon Jones Martian
Employee ID: 12345



When you convert the PDF to a text string, the second example above is transformed into the one-line format of the first.

Next, even if we know this user data layout format, a PDF is compressed data, so you cannot just extract this content without work. Choices are to use Apple's PDFKit framework where one can work on the PDF natively as text, and match the user data content using Objective-C. That would be the fastest, but one can also tell Automator to further extract the individual PDF page content to text files, where one avoids Objective-C, but then must use regular expressions to match the user data. Then use the name and ID content to rename the corresponding PDF page. This is still difficult to support using macOS UNIX tools, as the regular expression syntax has a long learning curve.

For step 3, there are no external tools that can batch set a PDF owner,user password, or other protections without using Apple's PDFKit framework with Objective-C. Not a pretty picture either.

No matter how you approach this, it is a programming/scripting solution that without that inherent knowledge, you will not be able to support it. You should find someone local that can do this for you, and provide relevant, enduring support.