There is no migration utility available as ispconfig 2 and 3 use a completely different setup and have different system requirements. You will have to recreate the email domains, websites, users etc. manually.
Regarding your update problem with ispconfig 2, please see the ISPConfig 2 release notes. There are a few additional packages neded for spamassassin for the latst releases. The /root/ispconfig folder is always deleted during update, you simply have to run "mkdir /root/ispconfig" and then run the setup script again to redo the update, ispconfig will rebuild the /root/ispconfig folder then automatically. So your ispconfig 2 system is not broken, ispconfig 2 is just not fully updated yet.