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.