You mentioned before you are running
Here are some good settings to start with
innodb_buffer_pool_size=4G
innodb_buffer_pool_instance=2
innodb_read_io_threads=12
innodb_write_io_threads=12
innodb_io_capacity=300
innodb_log_file_size=128M
Don't do the conversion yet !!!
Put there settings in my.cnf, then do the following
service mysql stop
cd /var/lib/mysql
rm -f ibdata1 ib_logfile*
service mysql start
Now, you can do the conversion.
Give it a Try !!!
UPDATE 2013-05-10 10:44 EDT
Here are my past posts on tuning InnoDB for better CPU usage
Here are my past posts on tuning InnoDB