G4 PowerMac can't see forth drive?

Sorry, I just realized I posted this in the wrong place earlier today.
I recently installed a new 500GB drive into a G4 PowerMac tower. This is the forth drive in the system and required the removal of the old CDROM drive in the system. It's not an issue as the cdrom is never used and there's external ones we can connect in a pinch. Originally I thought that the new 500GB drive was used as a backup and integrated into the RAID because I was reading the display in DiskUtility wrong. However, I came to realize this wasn't the case and it is not actually detected by the system at all (I'm fairly sure it's not a jumper problem either.) There is the original 40GB drive in it as the OS drive, as well as two 250GB drives used in a RAID 1 (mismatched, a WD 2500JB-00GVC0, and a ST325620A).
Is it possible that since I simply removed the CDROM and installed a hard drive, Mac OS X is waiting for "media" to be inserted? The computer serves as a fileserver which is needed pretty much all of the time so I don't often have the chance until late at night to bring it down to open it up. I have not yet tried booting it up without the CDROM and then reinstalling the drive and booting it up again.
I've not yet tried resetting the nvram or pram on the computer to see if this causes the machine to reset itself.

Dan,
Can you confirm it's an MDD G4, right forum, but everywhere just describes your Mac as a G4 PowerMac. The MDD was the very last G4 PowerMac.
I have serious doubts that it is for two reasons:
if the original boot disk is 40GB.
if you only have space for 3 disks on the existing ATA/66 and (presumably) ATA/100 bus.
That means your built-in ATA bus wouldn't be able to see drives over 128GB. Not sure how your RAID works, unless you have a PCI card that offers 48 bit LBA support.
Even if you did have an MDD, I'm almost certain that the ATA/33 bus for optical drives doesn't support drives over 128GB.

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