I am making changes in the bootstrap script the require a reboot before Director can continue. How can I do that?
Otherwise there will not be enough space for all the parcels to be deployed onto the target instance.
While a bootstrap script can issue a reboot, I don't think Director will reliably handle all of the ways that could play out. For example, if the reboot happens so quickly that it cuts off script execution, then Director will think the script failed, and retry it, and possibly run out of retries before the instance comes back. And if it does come back, it'll run the script again, and reboot again.
If the bootstrap script is just adding disk space, you do have other options. An EC2 instance template can specify extra EBS volumes, for example, and you can update mount points (without rebooting) to hook them in where necessary in the directory tree. Also, Director automatically attempts to resize the root partition to take up all the available disk space, so a separate script isn't necessary for that work.