I've upgraded to level-2 but now my SP doesn't work anymore
First of all...Level-2 federation requires either you have commercial certificates or you use AusCert? certificate for SP's back-end communication.
Common problems are:
you use unacceptable certificate (i.e. using level-1 cert for SP registered on level-2)
you use certificate signed with wrong purpose
openssl x509 -purpose -in /etc/certs/mycert.pem
you need client-ssl capable certificate in order for it to communicate to another server (i.e. IdP)
most commercial certificate has both client-ssl and server-ssl purposes, however, some will only issue server-ssl (i.e. free IPSCA for education-only cert is server-ssl only)
it could be not related to certificate at all, could be simply your registration at the federation is wrong (i.e. have you checked your correct entityId, or modified your shibboleth.xml according to migration path to level-2?)