First, for a CentOS 7 server, /usr/local/moodle is a strange location for moodle code. CentOS 7 is Linux Standards Base distro which means apache config (httpd.conf) default would make /var/www/ apache users home directory. In there, an html which is typically document root as defined in main config file for apache. /etc/httpd/conf/httpd.conf on typical setup.
Having moodle in /usr/local/ would mean there are or should be other config files that define that directory. Do you have a special config file for that location or have you changed httpd.conf such that /usr/local/ is now apache home?
Plugin removal best done by Moodle Admin interface, but in the cases of plugins that have dependencies (require other plugins), one might have to resort to manually moving the plugin folders out to an archive directory, then visiting plugins via Moodle Admin interface ... it will say missing from disk ... that's ok, click the 'Upgrade Database' button and that should remove rows in mdl_config_plugins table that refer to those plugins.
In what you shared back about owner ... daemon,daemon???? The user for apache on CentOS 7 is typically 'apache' ... as defined in main config file /etc/httpd/conf/httpd.conf
A failed attempt to upgrade will mess with DB tables some so you might have to restore your DB to when site was running older version.
Hope you did a site backup ... code + DB minimally ... so you can restore and 'try it again'.
The next try, make sure you have debugging turned on from the get go.
What documents are you following for upgrading?
When your site was a 3.6, did you check server environment and update the component. Then picked 3.8 as destination version to see if there were any reported issues concerning environment?
BTW, you never did answer the question about that strange file name ... ending with .pgp in moodle code related to navigation. That's why I ask about what docs you are following for upgrading.