Hmmm, ok well you have the basics right it seems.
I did some looking around and found this link which may help - http://forum.mikrotik.com/t/solved-l2tp-ipsec-stoped-working-after-upgrade-to-6-18/79942/1
I wonder if you have some peer settings left over from earlier attempts.
Try the following and see if it helps…
- Disable IPSEC in the EoIP settings by removing the “secret’s”.
- Remove any Ipsec Peers and policy’s. You will not be able to remove the default Policy

- Test that traffic flows ok.
- Now add in secrets to EoIP and check ipsec peers and policys. There should be a dynamic peer and dynamic policy created. Also check the default proposal on both routers match.
- Retest and see if your tunnels come up OK.