Can you swap connectors on the mobo from the working ones to the non-working ones to see if its a mobo issue... or the bays? Seems unlike two bays would go out... right next to each other... either a connection... or a bad mobo?
If all of the cables are tight on both the logic board end and the where the drive sleds plug in from what I've been reading it's a bad logic board, they call it the backplane board too.
It seems like a common problem.
You can get an internal SATA card for around $30, Rocket620A. Macmall has them so they are OS X compatible, but OWC has them cheaper. I don't know if the wiring you have can be re-routed or if you can use the cables that come with it to attach to the back of the sled holder. Supposedly this one works in a Mac Pro. Not sure if it's bootable tough.
I did not even think about SATA card! I have one in my QuickSilver that may work in the PCI Express slot.
The hard drives slide into the connectors on the logic board though. I will have to look and see I can turn the hard drive around and have the connections from the card.
Here is an image of what the logic board connection looks like (ODD-the two connectors on the upper right hand side. There are just two so I am guessing each one is for two bays. I did not try switching them...have to take the fan out for that.)
Here is where the HD sled slides in. On the blue circuit board on my third bay there is a magic marker mark:
The Quicksilver card won't work. I'm also wondering about how you'll get power to the drives. The connectors on the PCI E card are for data.
Instead of having to turn the hard drives around backwards, I wonder if you can remove the two screws on the connectors at the end of the sled holder. Do those cables come off, or are they soldered into that connector.
The power is a good question. The QuickSilver card has a data and a power cable. The power cable connected to the old style IDE power connector. It looks the newer cards have the place for the data and power cable. I know for the external PCI card, I am thinking the data for the newer cards would plug into the logic board from on the two empty connectors marked ODD_SATA. The other two empty connectors to their right is were my video card power plugs in.
I am not sure what is behind the connectors for the sled.
ODD = Optical Disc Drive. From what I've read it will work with HDs, but they are not bootable is all.
So if you could get power to the 3rd HD, along with a SATA data cable on one of the ODD SATA connectors you may not need a card.
Will the cable from the 3rd sled running to the logic board stretch to the ODD SATA connector? I wonder if the SATA connector is bad on the board, or if it's not getting power to the drive, can you hear the new drive spin up or see a light on it?
Maybe get SATA data and/or power extension cables?
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