According to Protocol 006_PsCARTHA Carthage documentation:
The baking daemon requires direct access to the context of the Tezos node. The daemon for 006 requires the new context introduced by Irmin2. As such bakers that use the default baker need to upgrade to the new storage backend in order to be able to run the 006 baking daemons.
Would /.tezos-node/version.json/0.0.4 indicate that I am running the upgraded storage version?