Just to chime in here. I agree that double NAT is best avoided but it only gives trouble in rare circumstances. I have run double NAT for months with no problems at all.
This is not a double NAT problem.
You don't seem to have fully explored the packet capture that showed that pfSense was not NATing traffic. Simply switching from auto to manual should not stop NAT working. You would have to deliberately remove the NAT rules.
Switch it back to auto, I would reboot the box at this point, then rerun your packet captures to demonstrate that NAT is working.
Also unexplained is the fact that you somehow ended up without a default route? :-\
Going right back to the beginning; is it a specific set of configuration changes that cause pfSense to stop forwarding traffic or simply making too many changes of any sort?
Steve