I didn't think you could still have Mac Classic with Leopard, but I could be wrong. If your HDD is supporting two partitions, that was definitely slow things down, especially on your older hardware.
First of all, back everything up to an external drive - Your home folder and any applications you downloaded. Make sure you have everything safe. Then, as others have said, start the install process again with archive and install (this will double your backup protection) - or you could just wipe and install. But you really need to repartition your drive to a single partition, so OS 9 is not on there. I am sure this will be holding you back. If you don't use OS 9 at all anymore, and don't need any files, just remove it, otherwise if you do, you need to boot to it and put those things safe.