Use the user data to pass a script to a new EC2 Instance. I am not sure if you can start a pre-existing instance and pass it data.
I have a pre-configured AMI that has a script saved on the root drive.  This script is used to configure the server and download the latest source.
So your request could look like the following:
var runInstance = new RunInstancesRequest();
        runInstance.WithImageId("{ami-id}")
            .WithInstanceType("{size}")
            .WithMaxCount(1)
            .WithMinCount(1)
            .WithSecurityGroup("{the security group}")
            .WithKeyName("{your key}")
            .WithUserData(Convert.ToBase64String(Encoding.ASCII.GetBytes(userData)));
        ec2.RunInstances(runInstance);
The user data can contain either a reference to a script or the script itself.