If you have migrated the articles and issues manually, the ids for the galleys, articles, issues, and journal have probably changed, not just the journal id. This will prevent the usage stats tool from rebuilding the metrics table successfully from the logs with the old ids. It will also mean that if you were to migrate the metrics table directly, you would have to translate the assoc_ids for all of these objects.
The only current methodology for moving form a multi-journal install to a single journal install is to copy the entire multijournal install and then delete every other journal.
The PKP Technical Committee is actively discussing better ways to migrate data from one install to another.