To resolve the Autoconfig error, please apply the following steps:
1) Obtain the newer versions of the conflicting files. Using the errors provided here as examples:
/<AD_TOP>/admin/template/CGIcmd.dat(version: 115.11)
/<FND_TOP>/11.5.0/admin/template/apps_ux.conf(version: 115.49)
2) Use these newer versions to re-customize them, and place them back in the respective custom template locations.
3) Run AutoConfig.