linux Server Security with WHM Panel

I have a Linux server with WHM and Cpanel with bitninja Server security. but we face some unusual high load on server. So we are going to purchase new server but we want to set extra security layer on our server. Also Want to block all Port except HTTP, HTTPS, Mysql, Bitninja and some imports will open.
We will host CodeIgniter Web portal with mysql db.
*** now we seen some index file create automatic outside public html

Can anyone help me to secure my server