How about going to actual official Mikrotik wiki and using guides from there?
Also users in Mikrotik forum posted few as well. e.g. I created this: http://forum.mikrotik.com/t/mikrotik-behind-nat-to-mikrotik-ipsec-ike2-with-certs-tunnel-eoip/144952/1 + http://forum.mikrotik.com/t/vpn-ipsec-with-strongswan/132391/1
One of the best guides online I found is from https://mynetworktraining.com/ this guy which also has all the courses on Udemy too, including setting up VPNs.