One thing you might examine is your waits for the various files. If you see waits stacking up, then you have IO issues.
A few more references for you:
http://www.simple-talk.com/sql/performance/a-performance-troubleshooting-methodology-for-sql-server/
http://www.sqlskills.com/blogs/paul/post/capturing-wait-stats-for-a-single-operation.aspx