To put it simply, I want a stackscript to do some things, reboot, then continue where it left off and finish.

Any suggestions?

The StackScript itself needs to exit for the SS environment to clean up, else the SS will re-execute -- so if you want to reboot you need to somehow 'schedule' it (temporary cron job, fork a process with a delay-before-rebooting, etc). Setting up what to happen after that step will be up to you.

-Chris