The A4000T does have an IDE controller.
You shouldn't need to disable the SCSI controller. I'm not sure whether it can be disabled.
Delays can be caused when you are booting with a CD drive attatched, or when you have devices attatched to both the IDE controller AND SCSI controller.
I'm not sure, but it could be possible that delays are caused by having devices on two different controllers.
Extra devices will only slow things down.
A bit of advice:
1. Try booting with only on HDD
2. Check the device ID's. Make sure that they don't conflict (for each controller)
