When uninstalling software you compiled yourself you can run make -n install to see what the make install command did. For Nginx you only had to remove /sbin/nginx before installning NginX from YUM.
# make -n install make -f objs/Makefile install make[1]: Entering directory `/root/install/cache/nginx-1.9.9' test -d '/' || mkdir -p '/' test -d '/' || mkdir -p '/' test ! -f '/sbin' || mv '/sbin' '/sbin.old' cp objs/nginx '/sbin' test -d '/etc/nginx' || mkdir -p '/etc/nginx' cp conf/koi-win '/etc/nginx' cp conf/koi-utf '/etc/nginx' cp conf/win-utf '/etc/nginx' test -f '/etc/nginx/mime.types' || cp conf/mime.types '/etc/nginx' cp conf/mime.types '/etc/nginx/mime.types.default' test -f '/etc/nginx/fastcgi_params' || cp conf/fastcgi_params '/etc/nginx' cp conf/fastcgi_params '/etc/nginx/fastcgi_params.default' test -f '/etc/nginx/fastcgi.conf' || cp conf/fastcgi.conf '/etc/nginx' cp conf/fastcgi.conf '/etc/nginx/fastcgi.conf.default' test -f '/etc/nginx/uwsgi_params' || cp conf/uwsgi_params '/etc/nginx' cp conf/uwsgi_params '/etc/nginx/uwsgi_params.default' test -f '/etc/nginx/scgi_params' || cp conf/scgi_params '/etc/nginx' cp conf/scgi_params '/etc/nginx/scgi_params.default' test -f '/etc/nginx/nginx.conf' || cp conf/nginx.conf '/etc/nginx/nginx.conf' cp conf/nginx.conf '/etc/nginx/nginx.conf.default' test -d '/var/run/nginx' || mkdir -p '/var/run/nginx' test -d '/var/log/nginx/access' || mkdir -p '/var/log/nginx/access' test -d '//html' || cp -R html '/' test -d '/var/log/nginx/errors' || mkdir -p '/var/log/nginx/errors' make[1]: Leaving directory `/root/install/cache/nginx-1.9.9'
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