Unable to install Pathauto, pathauto.settings already exists in active configuration
Before trying to do whatever I suggest below first of all have a full backup of the site.
It seems pathauto module is not uninstalled properly.
To solve your problem you can just delete the pathauto.settings from config using drush.
Use the below command to delete the conflicting config.
drush cdel pathauto.settings
It will delete the existing pathauto configuration.Then you can install the pathauto module.
You should consider using composer for the module management.