You should make sure that the port rules do exactly what you want them to do, including packaging up the port. These are the important points you need to verify.
pkg-plist does not contain anything not installed by your port
pkg-plist contains everything that is installed by your port
Your port can be installed multiple times using the reinstall target
Your port cleans up after itself upon deinstall
Recommended test ordering
Make sure that there are not any warnings issued in any of the package and deinstall stages. After step 3, check to see if all the new directories are correctly deleted. Also, try using the software after step 4, to ensure that it works correctly when installed from a package.