Why not build a cage that can take 2 or even 3 hard drives side by side sacrificing 2 PCI slots? The cage can be suspended using the screw holes for the now useless PCI slots and the PCI card guide groves. This leaves one PCI slot for an IDE or SCSI card.
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The most difficult part is heat issue. This PCI compartiment was scheduled or air cooling around PCI cards which are thinner than HD. I am nearly sure that Apple will avoid his warranty if such a trick was performed.