Whenever your hacked it's best to check for all types of Malicious files/codes etc instead of simply assuming it was one "file" as it were, for that try the info outlined here:
http://www.vbulletin.com/forum/blogs...iller/3934768- especially run the queries to see if anything comes up.
On the one file you had trouble deleting, open a support ticket with your host and mention this to them, ask them to verify that the file was removed entirely - they may at that point decide to run some server-side scans it depends on your host and what importance they place on matters such as this.