"Security groups (which define what IPs can access what ports, similar to basic IPTables firewall rules) cannot be shared between EC2-Classic and EC2-VPC,"
That is no longer true. In December 2014 Amazon launched ClassicLink, which lets you add EC2-Classic instances to VPC security groups.
https://aws.amazon.com/blogs/aws/classiclink-private-communi...
http://www.youtube.com/watch?v=HexrVfuIY1k&t=33m33s