Hello,
Besides performance questions may I emphasize on the non robustness of the innodb mode. Reccntlty I have lost the whole content of a Wiki (naively, how could I know?) saved while mysql was running. The other wiki using MyISAM has been recovered. This very fragile innodb behaviour is inacceptable.
Did you remove 'ibdata' file manually? That is the major common reason of 'data lost' with InnoDB.