After waiting for nearly an hour for the database to be deleted I have now completed the upgrade to version 2.9.2 of WordPress!
Thankfully, once the new database had been created (this time a flashy new MySQL v5 database) it was all easy. Edited the wp-config to point to the new database, exported the old database and imported the data into the new one, ran some tests and all was running well!
The WordPress Auto Upgrade then ran completely smoothly.
Hopefully with MySQL now running on v5 the next upgrade will have no problems what-so-ever. Well, we will see!!