Thanks!
I just logged into the machine locally as root and everything works correctly.
So I think it is clearly just an issue with the user account that I'm using to SSH with. Now thinking about it more rationally, it makes sense. The folders that I'm getting permission errors with are those that are asterisk/asterisk and the account isn't apart of that group. This explains why the MOTD banner wasn't showing either.
I was afraid something was wrong because I have another Stable 12 Distro installation that I use a non-root account to SSH in with, passwords off and only accept connections using key based authentication. I had never seen those errors before. However I set it up years ago so maybe I added it to the asterisk group and forgot.
EDIT:
I just checked my FreePBX 12 server. Something must have changed with permissions moving to 13? My SSH account on that server is NOT a member of the asterisk group. HOWEVER /etc/asterisk shows different permission on that server (particularly read/execute permissions for Other). Either they changed from 12 to 13, or I changed them on this 12 server and don't remember.
[jayg30@pbx1 ~]$ ls -al /etc/asterisk/
total 632
drwxrwxr-x. 3 asterisk asterisk 12288 Aug 10 09:58 .
drwxr-xr-x. 93 root root 12288 Nov 4 19:42 ..
-rwxrwxr-x 1 asterisk asterisk 665 Nov 4 22:27 ari_additional.conf
-rwxrwxr-x 1 asterisk asterisk 0 Aug 20 17:09 ari_additional_custom.conf
lrwxrwxrwx 1 asterisk asterisk 51 Aug 20 17:09 ari.conf -> /var/www/html/admin/modules/arimanager/etc/ari.conf
-rwxrwxr-x 1 asterisk asterisk 684 Nov 4 22:27 ari_general_additional.conf
-rwxrwxr-x 1 asterisk asterisk 0 Aug 20 17:09 ari_general_custom.conf
-rwxrwxr-x. 1 asterisk asterisk 335 Feb 27 2014 asterisk.conf
lrwxrwxrwx. 1 asterisk asterisk 48 Feb 27 2014 ccss.conf -> /var/www/html/admin/modules/campon/etc/ccss.conf
-rwxrwxr-x. 1 asterisk asterisk 664 Nov 4 22:27 ccss_general_additional.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 ccss_general_custom.conf
-rwxrwxr-x. 1 asterisk asterisk 91 Feb 27 2014 cdr_adaptive_odbc.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 cdr.conf
-rwxrwxr-x. 1 asterisk asterisk 699 Feb 27 2014 cdr_mysql.conf
-rwxrwxr-x. 1 asterisk asterisk 699 Feb 27 2014 cdr_mysql.conf.bak
lrwxrwxrwx. 1 asterisk asterisk 44 Feb 27 2014 cel.conf -> /var/www/html/admin/modules/cdr/etc/cel.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 cel_custom_post.conf
-rwxrwxr-x. 1 asterisk asterisk 712 Nov 4 22:27 cel_general_additional.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 cel_general_custom.conf
lrwxrwxrwx. 1 asterisk asterisk 49 Feb 27 2014 cel_odbc.conf -> /var/www/html/admin/modules/cdr/etc/cel_odbc.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 cel_odbc_custom.conf
-rwxrwxr-x. 1 asterisk asterisk 664 Nov 4 22:27 chan_dahdi_additional.conf
-rwxrwxr-x. 1 asterisk asterisk 766 Feb 27 2011 chan_dahdi.conf
-rwxrwxr-x. 1 asterisk asterisk 715 Feb 27 2014 chan_dahdi.conf.template
-rwxrwxr-x. 1 asterisk asterisk 664 Nov 4 22:27 confbridge_additional.conf
lrwxrwxrwx. 1 asterisk asterisk 59 Feb 27 2014 confbridge.conf -> /var/www/html/admin/modules/conferences/etc/confbridge.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 confbridge_custom.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 dahdi-channels.conf
lrwxrwxrwx 1 asterisk asterisk 57 Feb 26 2014 directorypro -> /var/www/html/admin/modules/directorypro/etc/directorypro
-rwxrwxr-x. 1 asterisk asterisk 50 Feb 27 2014 enum.conf
-rwxrwxr-x. 1 asterisk asterisk 277755 Nov 4 22:27 extensions_additional.conf
lrwxrwxrwx. 1 asterisk asterisk 52 Feb 27 2014 extensions.conf -> /var/www/html/admin/modules/core/etc/extensions.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 extensions_custom.conf
-rwxrwxr-x. 1 asterisk asterisk 2671 Feb 27 2014 extensions_custom.conf.sample
-rwxrwxr-x 1 asterisk asterisk 10445 May 14 17:56 extensions_override_fop2.conf
-rwxrwxr-x. 1 asterisk asterisk 53 May 14 17:56 extensions_override_freepbx.conf
-rwxrwxr-x 1 asterisk asterisk 0 May 14 17:56 extensions_override_freepbx.conf.bak
-rwxrwxr-x. 1 asterisk asterisk 708 Nov 4 22:27 features_applicationmap_additional.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 features_applicationmap_custom.conf
lrwxrwxrwx. 1 asterisk asterisk 50 Feb 27 2014 features.conf -> /var/www/html/admin/modules/core/etc/features.conf
-rwxrwxr-x. 1 asterisk asterisk 701 Nov 4 22:27 features_featuremap_additional.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 features_featuremap_custom.conf
-rwxrwxr-x. 1 asterisk asterisk 679 Nov 4 22:27 features_general_additional.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 features_general_custom.conf
-rwxrwxr-x. 1 asterisk asterisk 1494 Feb 27 2014 freepbx_featurecodes.conf.template
-rwxrwxr-x. 1 asterisk asterisk 965 Feb 27 2014 freepbx_menu.conf.template
-rwxrwxr-x. 1 asterisk asterisk 730 Feb 27 2014 freepbx_module_admin.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 globals_custom.conf
-rwxrwxr-x 1 asterisk asterisk 741 Nov 4 22:27 http_additional.conf
lrwxrwxrwx 1 asterisk asterisk 46 Feb 26 2014 http.conf -> /var/www/html/admin/modules/core/etc/http.conf
-rwxrwxr-x 1 asterisk asterisk 0 Feb 26 2014 http_custom.conf
-rwxrwxr-x. 1 asterisk asterisk 846 Nov 4 22:27 iax_additional.conf
lrwxrwxrwx. 1 asterisk asterisk 45 Feb 27 2014 iax.conf -> /var/www/html/admin/modules/core/etc/iax.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 iax_custom.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 iax_custom_post.conf
-rwxrwxr-x. 1 asterisk asterisk 830 Nov 4 22:27 iax_general_additional.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 iax_general_custom.conf
-rwxrwxr-x. 1 asterisk asterisk 664 Nov 4 22:27 iax_registrations.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 iax_registrations_custom.conf
-rwxrwxr-x. 1 asterisk asterisk 844 Nov 4 22:27 indications.conf
lrwxrwxrwx 1 asterisk asterisk 45 Feb 26 2014 ivrpro -> /var/www/html/admin/modules/ivrpro/etc/ivrpro
drwxrwxr-x 2 asterisk asterisk 4096 Dec 5 2014 keys
-rwxrwxr-x. 1 asterisk asterisk 664 Nov 4 22:27 localprefixes.conf
lrwxrwxrwx 1 asterisk asterisk 52 Feb 26 2014 logger.conf -> /var/www/html/admin/modules/logfiles/etc/logger.conf
-rwxrwxr-x. 1 asterisk asterisk 735 Nov 4 22:27 logger_general_additional.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 logger_general_custom.conf
-rwxrwxr-x. 1 asterisk asterisk 789 Nov 4 22:27 logger_logfiles_additional.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 logger_logfiles_custom.conf
-rwxrwxr-x. 1 asterisk asterisk 773 Nov 4 22:27 manager_additional.conf
-rwxrwxr-x 1 asterisk asterisk 1013 Sep 27 2014 manager.conf
-rwxrwxr-x 1 asterisk asterisk 997 Aug 23 2014 manager.conf.12.0.1.bak
-rwxrwxr-x. 1 asterisk asterisk 930 Feb 27 2014 manager.conf.bak
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 manager_custom.conf
-rwxrwxr-x. 1 asterisk asterisk 686 Nov 4 22:27 meetme_additional.conf
-rwxrwxr-x. 1 asterisk asterisk 40 Feb 27 2014 meetme.conf
-rwxrwxr-x. 1 asterisk asterisk 1774 Feb 27 2014 modem.conf
-rwxrwxr-x. 1 asterisk asterisk 2527 Nov 4 22:27 modules.conf
-rwxrwxr-x. 1 asterisk asterisk 2393 Feb 27 2014 modules.conf.2.8.0-1.bak
-rwxrwxr-x 1 asterisk asterisk 691 Nov 4 22:27 motif.conf
-rwxrwxr-x 1 asterisk asterisk 691 Sep 27 2014 motif.conf.bak
-rwxrwxr-x 1 asterisk asterisk 0 Sep 27 2014 motif_custom.conf
-rwxrwxr-x. 1 asterisk asterisk 808 Nov 4 22:27 musiconhold_additional.conf
-rwxrwxr-x. 1 asterisk asterisk 208 Feb 27 2014 musiconhold.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 musiconhold_custom.conf
-rwxrwxr-x. 1 asterisk asterisk 1418 Feb 27 2014 phone.conf
-rwxrwxr-x. 1 asterisk asterisk 90 Feb 27 2014 phpagi.conf
-rwxrwxr-x 1 asterisk asterisk 696 Nov 4 22:27 pjsip.aor.conf
-rwxrwxr-x 1 asterisk asterisk 0 Nov 18 2014 pjsip.aor_custom.conf
-rwxrwxr-x 1 asterisk asterisk 0 Jul 28 09:38 pjsip.aor_custom_post.conf
-rwxrwxr-x 1 asterisk asterisk 697 Nov 4 22:27 pjsip.auth.conf
-rwxrwxr-x 1 asterisk asterisk 0 Nov 18 2014 pjsip.auth_custom.conf
-rwxrwxr-x 1 asterisk asterisk 0 Jul 28 09:38 pjsip.auth_custom_post.conf
-rwxrwxr-x 1 asterisk asterisk 1163 Nov 4 22:27 pjsip.conf
-rwxrwxr-x 1 asterisk asterisk 0 Nov 18 2014 pjsip_custom.conf
-rwxrwxr-x 1 asterisk asterisk 0 Sep 27 2014 pjsip.custom.conf
-rwxrwxr-x 1 asterisk asterisk 701 Nov 4 22:27 pjsip.endpoint.conf
-rwxrwxr-x 1 asterisk asterisk 0 Nov 18 2014 pjsip.endpoint_custom.conf
-rwxrwxr-x 1 asterisk asterisk 0 Jul 28 09:38 pjsip.endpoint_custom_post.conf
-rwxrwxr-x 1 asterisk asterisk 701 Nov 4 22:27 pjsip.identify.conf
-rwxrwxr-x 1 asterisk asterisk 0 Nov 18 2014 pjsip.identify_custom.conf
-rwxrwxr-x 1 asterisk asterisk 0 Jul 28 09:38 pjsip.identify_custom_post.conf
-rwxrwxr-x 1 asterisk asterisk 0 Sep 27 2014 pjsip.manualtrunks.conf
-rwxrwxr-x 1 asterisk asterisk 733 Nov 4 22:27 pjsip_notify.conf
-rwxrwxr-x 1 asterisk asterisk 705 Nov 4 22:27 pjsip.registration.conf
-rwxrwxr-x 1 asterisk asterisk 0 Nov 18 2014 pjsip.registration_custom.conf
-rwxrwxr-x 1 asterisk asterisk 0 Jul 28 09:38 pjsip.registration_custom_post.conf
-rwxrwxr-x 1 asterisk asterisk 915 Nov 4 22:27 pjsip.transports.conf
-rwxrwxr-x 1 asterisk asterisk 0 Nov 18 2014 pjsip.transports_custom.conf
-rwxrwxr-x 1 asterisk asterisk 0 Jul 28 09:38 pjsip.transports_custom_post.conf
-rwxrwxr-x. 1 asterisk asterisk 81 Feb 27 2014 privacy.conf
-rwxrwxr-x 1 asterisk asterisk 1021 May 13 19:19 prosody_additional.conf
-rwxrwxr-x 1 asterisk asterisk 664 Mar 27 2015 queuerules_additional.conf
lrwxrwxrwx 1 asterisk asterisk 54 Feb 26 2014 queuerules.conf -> /var/www/html/admin/modules/vqplus/etc/queuerules.conf
-rwxrwxr-x 1 asterisk asterisk 0 Feb 26 2014 queuerules_custom.conf
-rwxrwxr-x. 1 asterisk asterisk 1326 Nov 4 22:27 queues_additional.conf
-rwxrwxr-x. 1 asterisk asterisk 522 Feb 27 2014 queues.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 queues_custom.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 queues_custom_general.conf
-rwxrwxr-x. 1 asterisk asterisk 743 Nov 4 22:27 queues_general_additional.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 queues_post_custom.conf
-rwxrwxr-x 1 asterisk asterisk 0 Feb 26 2014 res_digium_phone_additional.conf
-rwxrwxr-x 1 asterisk asterisk 0 Feb 26 2014 res_digium_phone_applications.conf
lrwxrwxrwx 1 asterisk asterisk 67 Feb 26 2014 res_digium_phone.conf -> /var/www/html/admin/modules/digium_phones/etc/res_digium_phone.conf
-rwxrwxr-x 1 asterisk asterisk 0 Feb 26 2014 res_digium_phone_devices.conf
-rwxrwxr-x 1 asterisk asterisk 0 Feb 26 2014 res_digium_phone_firmware.conf
-rwxrwxr-x 1 asterisk asterisk 0 Feb 26 2014 res_digium_phone_general.conf
-rwxrwxr-x 1 asterisk asterisk 733 Nov 4 22:27 res_fax.conf
-rwxrwxr-x 1 asterisk asterisk 0 Feb 26 2014 res_fax_custom.conf
-rwxrwxr-x 1 asterisk asterisk 720 Nov 4 22:27 res_fax_digium.conf
-rwxrwxr-x 1 asterisk asterisk 0 Feb 26 2014 res_fax_digium_custom.conf
-rwxrwxr-x. 1 asterisk asterisk 802 Nov 4 22:27 res_odbc_additional.conf
lrwxrwxrwx. 1 asterisk asterisk 50 Feb 27 2014 res_odbc.conf -> /var/www/html/admin/modules/core/etc/res_odbc.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 res_odbc_custom.conf
-rwxrwxr-x 1 asterisk asterisk 884 Nov 4 22:27 res_parking.conf
-rwxrwxr-x. 1 asterisk asterisk 768 Nov 4 22:27 rtp_additional.conf
lrwxrwxrwx. 1 asterisk asterisk 45 Feb 27 2014 rtp.conf -> /var/www/html/admin/modules/core/etc/rtp.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 rtp_custom.conf
-rwxrwxr-x. 1 asterisk asterisk 14833 Nov 4 22:27 sip_additional.conf
lrwxrwxrwx. 1 asterisk asterisk 45 Feb 27 2014 sip.conf -> /var/www/html/admin/modules/core/etc/sip.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 sip_custom.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 sip_custom_post.conf
-rwxrwxr-x. 1 asterisk asterisk 1491 Nov 4 22:27 sip_general_additional.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 sip_general_custom.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 sip_nat.conf
-rwxrwxr-x. 1 asterisk asterisk 1798 Nov 4 22:27 sip_notify_additional.conf
lrwxrwxrwx. 1 asterisk asterisk 52 Feb 27 2014 sip_notify.conf -> /var/www/html/admin/modules/core/etc/sip_notify.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 sip_notify_custom.conf
lrwxrwxrwx 1 asterisk asterisk 71 Feb 26 2014 sip_notify_endpointman.conf -> /var/www/html/admin/modules/endpointman/etc/sip_notify_endpointman.conf
-rwxrwxr-x. 1 asterisk asterisk 754 Nov 4 22:27 sip_registrations.conf
-rwxrwxr-x. 1 asterisk asterisk 0 Feb 27 2014 sip_registrations_custom.conf
lrwxrwxrwx 1 asterisk asterisk 47 Feb 26 2014 udptl.conf -> /var/www/html/admin/modules/core/etc/udptl.conf
-rwxrwxr-x 1 asterisk asterisk 0 Feb 26 2014 udptl_custom.conf
-rwxrwxr-x. 1 asterisk asterisk 15 Feb 27 2014 version
-rwxrwxr-x. 1 asterisk asterisk 543 Nov 4 22:27 vm_email.inc
-rwxrwxr-x. 1 asterisk asterisk 1048 Nov 4 22:27 vm_general.inc
-rwxrwxr-x 1 asterisk asterisk 3530 Oct 7 09:19 voicemail.conf
-rwxrwxr-x. 1 asterisk asterisk 67 Feb 27 2014 voicemail.conf.template
-rwxrwxr-x 1 asterisk asterisk 736 Nov 4 22:27 xmpp.conf
-rwxrwxr-x 1 asterisk asterisk 736 Sep 27 2014 xmpp.conf.bak
-rwxrwxr-x 1 asterisk asterisk 0 Sep 27 2014 xmpp_custom.conf
-rwxrwxr-x 1 asterisk asterisk 0 Sep 27 2014 xmpp_general_custom.conf
-rwxrwxr-x. 1 asterisk asterisk 699 Feb 27 2014 zapata.conf.template