Good that it is solved 
.
Very likely you (or the script) deleted the WAN interface list (why?) and the net result is:
/ip firewall filter
...
add action=drop chain=forward comment="defconf: drop all from WAN not DSTNATed" connection-nat-state=!dstnat connection-state=new in-interface-list=*2000010
....
/ip firewall nat
add action=masquerade chain=srcnat comment="defconf: masquerade" ipsec-policy=out,none out-interface-list=*2000010
Which may well be the part of the problem.
For next time, this is #21 in the list:
http://forum.mikrotik.com/t/gp-csa-for-mikrotik-devices/182176/1