Joe will be able answer this better than I can, but as far as I know, the only supported "customization" for the registration page is the optional registration agreement text you can use. If by "FB auth" you mean Facebook authentication, a number of other security pages would have to be modified in addition to registration, and site settings would almost certainly need to be stored, and then you are looking at a serious fork of the code, which is very much not recommended--you'll lose the ability to upgrade your sites without an error-prone re-merge of your customizations each time.
Besides the built-in database authentication, mojoPortal supports LDAP, database with fallback to LDAP, Windows Live, and Open ID authentication. I don't know if Joe wants to add even more authentication options, because each additional method adds another layer of complexity, but I'll let him speak to that. If he is interested, it may be that you can work with him to get your Facebook authentication code integrated into the mojoPortal core and thereby avoid the whole forking issue.
Jamie