Open the main file and in the Individual View add AFN to the list by right-clicking on Birth Place and selecting "Add or Modify Columns". Under Personal, add the AFN (Click on it and the click on ">".) It then becomes a column in the Individual View. "Add or Modify Columns" also allows you to click and drag the AFN to the top of the list of columns so it appears as the left-hand column. Open the second file in PAF and in Select Window menu > Tile Vertically to see both PAF files side by side. Sort the people by name, and you should be able to do what you want.
This may also be of interest to you. PAF Insight from http://ohanasoftware.comhttp://ohanasoftware.com has a "Compare and Synch" function that will compare two PAF databases and allow you to import people from the secondary database to the primary one. The price is about $25US. It is also handy for updating a PAF database from the IGI, seeing which individuals are unattached to families and which families are not attached to the main pedigree (family tree). It can also repair some database problems that PAF can't repair, you can change the RINs. It is the only product I know of that can compare and synchronize two PAF databases. That is the reason I bought it.