How do I make cloud-init startup scripts run every time my EC2 instance boots?

In 11.10, 12.04 and later, you can achieve this by making the 'scripts-user' run 'always'. In /etc/cloud/cloud.cfg you'll see something like:

cloud_final_modules:
 - rightscale_userdata
 - scripts-per-once
 - scripts-per-boot
 - scripts-per-instance
 - scripts-user
 - keys-to-console
 - phone-home
 - final-message

This can be modified after boot, or cloud-config data overriding this stanza can be inserted via user-data. Ie, in user-data you can provide:

#cloud-config
cloud_final_modules:
 - rightscale_userdata
 - scripts-per-once
 - scripts-per-boot
 - scripts-per-instance
 - [scripts-user, always]
 - keys-to-console
 - phone-home
 - final-message

That can also be '#included' as you've done in your description. Unfortunately, right now, you cannot modify the 'cloud_final_modules', but only override it. I hope to add the ability to modify config sections at some point.

There is a bit more information on this in the cloud-config doc at https://github.com/canonical/cloud-init/tree/master/doc/examples

Alternatively, you can put files in /var/lib/cloud/scripts/per-boot , and they'll be run by the 'scripts-per-boot' path.

In /etc/init.d/cloud-init-user-scripts, edit this line:

/usr/bin/cloud-init-run-module once-per-instance user-scripts execute run-parts ${SCRIPT_DIR} >/dev/null && success || failure

to

 /usr/bin/cloud-init-run-module always user-scripts execute run-parts ${SCRIPT_DIR} >/dev/null && success || failure

Good luck !