1) I remember seeing a thread in here that shows how to remove SW IDE driver. It's probably very simple but since I've never installed it, I don't know about removing it. I've read that this driver turns your IDE devices into SCSI devices. Some folks have slow booting like you while others have problem with CD burners. Without it, those folks are getting same benchmark scores.
2) For example, if you don't have an IDE device in Primary slave, then go to properties of Primary IDE Channel, Advanced Settings, Device 1, Device Type, set it to 'none'. Do the same for Secondary IDE Channel.
Let me know if you need more information.