Hello,
So I would usually advise you just upgrade the site opposed to create a J3 version and migrating.
But you can use SP Transfer, main thing to be concerned about is the Joomla! Categories table we use, ensure it is migrated exactly with the ID's etc.
Then just install the new version and all table changes etc will be done, we do checks on every update / install form the right tables/columns.
Many thanks
Tony