You’d like to add mod_security to your custom apache+mod_php build. The package requires a recent version of libxml2 which must be installed in parallel. Once compiled, httpd is unable to start as a result of missing symbols.
MySQL on RDS has its pros and cons. Only your organization can decide if the solution meets your needs. Migrating from a traditonal MySQL database to RDS may not be a simple task.
Believe it or not, VPC does not provide native NAT functionality. Hopefully, someday, we’ll get a NAT equivalent to IGW. Until then, NAT functionality is implemented through an EC2 NAT instance, usually running Linux.