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Ditto. I have four IDE drives and one SATA drive. As far as the motherboard, bios and OS are concerned, I've got 4 IDE ports, even though two of those are SATA.
As for the unplugging during install: I've got two different types of harddisks, so I can simply see the type during install. Only if you have two identical drives do you need to worry about it.
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