Android (Since 5.0 I think) no longer compresses everything just as a zip or system.img. You'll need to extract system.new.dat/system.dat (system partition) first before being able to access any content under /system.
Open up /system/lib in your Port ROM and copy all the files and folders. Paste them into the Base’s /system/lib directory, replacing all. Then go back to the Port ROM and delete the /system/lib folder, and replace it with the /system/lib folder from the Base ROM.
open system/build.prop from both the port and the base ROM in Notepad++. Update the Base build.prop to match the values for “ro.build.description=” and “ro.build.fingerprint=” from your Port. Now save the Base build.prop, exit Notepad++, and copy the Base build.prop into the Port ROM, overwriting the Port build.prop.
In Notepad++, open \META-INF\com\google\android\updater-script from both your base and port ROMs. Edit the Port’s script to be like the Base’s updater-script: specifically, change, edit, or add the sections for permissions, ui_prints, asserts, run_programs, and installing the kernel. Don’t change any of the symlinks. In the Port script, make sure that the ‘format’ values are appropriate for your device (compare them to the Base script).