Questions are showing up on email content, but not on PDF report.

When a completed form is emailed to both me, and my customer, I noticed that the form fields show correctly in the email, but some fields to not appear in the PDF. Is there a particular setting I need to adjust so ALL fields are included on the PDF?

Probably, you have deselected fields from your "Submissions" page:  https://www.jotform.com/help/269-How-to-View-Form-Submissions 

Example:

If not, try resetting your PDF report: https://www.jotform.com/help/384-How-to-Customize-PDF-Submissions-Report 

Let us know if you need more help, we will be glad to assist you.