Your original /etc files have been restored.
Review the differences between your old /etc and the new files stored in /etc/upgrade.
After you are sure that you have updated the /etc configuration files correctly and you have verified the system operation, the files in /etc/upgrade could be removed. If you are unsure, it would be better to leave the files there.
If a custom kernel is needed, compare your old kernel configuration file with the new GENERIC configuration file. Make the appropriate modifications for the new configuration file. Build the new kernel in the usual manner. Refer to the appropriate handbook section.
The /boot/kernel.config file is no longer needed if you build a custom kernel. The reference to it in /boot/loader.conf could be commented out (or deleted).
The upgrade process appends the new information to the file so you may see two references to the same things. The variables use the last value declared so only one is needed. Duplicates could be removed if desired.
Here is an example of what you might see:
# -- sysinstall generated deltas -- # userconfig_script_load="YES" # -- sysinstall generated deltas -- # userconfig_script_load="YES"