So my ISP seems to drop/reset the PPPoE connection about once a week for just a few moments. Whenever this happens, the router cannot seem to renegotiate IPSec for some reason. I am thinking something with a kernel route gets messed up, don't really know.

What is the method to add a script to the Mikrotik to cause the unit to reboot once it detects the PPPoE connection going down/back up?

Hello,

Try using tool > traffic monitor. You could add a script that reboots your router if traffic to pppoe-out is 0kbps...

The question is how to do this.
Any idee?

this will help:
http://wiki.mikrotik.com/wiki/Manual:To ... ic_Monitor

also you can use Netwatch ( you can ping Google DNS 8.8.8.8 or the ISP DNS...etc):
http://wiki.mikrotik.com/wiki/Netwatch