Mysql Server optimization tips needed! (InnoDB)
A few suggestions:


You might want to increase the size of your log files.  They are currently set to 250MB a piece.  A larger value there (perhaps a gig or two) should help reduce IO a bit.
Turn off the slow query logging
Decrease the buffer pool size a bit (or get more memory).  You might be starving threads for memory by using everything for the buffer pool.