Thanks very much Ken and Bret. All useful advice. The command line upgrade never got beyond the first output of --> system but as it turns out, my upgrade finally ran when I left it overnight, having shut down apache and started at the command line.
I will be turning on mysql logging and binary log in the hope of speeding up restore times that way. I do wonder if my database has some issues because it is not as fast as it might be as well as taking a long time to restore. My moodle has been running for about 4 years and has 500 courses.