The MySQL/InnoDB manual contains many hints for improving the performance of your system when using InnoDB tables. Apply as many of these as appropriate to your system.
You can start by looking here:
www.innodb.com/ibman.html#InnoDBTuning
On a noncritical server, cause MySQL to stop while you are halfway through a transaction. You should not need to drop your hard drives from a great height or kick the power plug out of the wall. Killing the process should be sufficient. Examine the binary log and see what happens when you restart the server.