How diagnose the extra SATA ports on the Mac Pro (early 2008) logic board?

I have had two SSDs in an OWC multi-mount in the second optical bay, one for Lion and one for Photoshop scratch. However, I recently began having intermittent boot problems. Sometimes there wouldn't be an Apple symbol upon boot/reboot, yet sometimes there would and the computer would boot. I have not experienced any crashes, kernel panics or such.
I thought the Lion SSD was faulty so installed Mountain Lion on the scratch drive, a Mercury Electra 3G which I have recently received as a replacement from OWC due to a previously faulty SSD. However, immediately there were boot problems from that SSD.
I have a feeling there is something wrong with the two extra SATA ports on the logic board. I am now booted off the Lion SSD placed in an external USB enclosure, which works but is a bit slower (I will get a bracket to install that SSD in the ordinary internal bays).
My question is how I can diagnose the logic board generally and specifically the extra SATA ports. I have Tech Tool Pro 6. I also thought I had AHT but on the Leopard DVD 1, which came with the Mac Pro (10.5.2) and on which AHT is supposed to be there is no trace of AHT. Odd. Booting from that DVD will only bring up the Leopard installer.
Btw I do think the Electra is broken because I am unable to boot ML from it in the USB enclosure.
Grateful for any ideas how to check my logic board.
Cheers
/p

If you could move the drives easily to another location then you could test the drives and also - make backup images! just to be safe. SSDs and their firmware and problems are almost all too common, even this last June a large issue with SandForce which OWC uses in some/most of theirs, and I get the feeling they are usually behind in testing and sending out firmware updates.
Corsair, Crucial and Intel have all had issues since it surfaced in May.
Diagnosing a motherboard with Apple Service Diagnostic CD is one thing. Swapping out SATA cables though no. WD Lifeguard does check communication to an SATA device drive and can - but you need to see the device in Windows or their boot CD (linux I imagine). Quite good utility though maybe not for an SSD.

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Time Machine’s Gory Details:
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https://support.apple.com/kb/HT1427
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http://www.apple.com/support/lion/installrecovery/
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I posted this incorrectly into the MacBook Pro so I have reposted here:
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TIA
Message was edited by: flommer

Hi flommer,
by default Windows or better said the Apple BootCamp Drivers for Windows can not see or use the odd SATA ports.
Have a look here http://osx86.net/archive/index.php/t-3159.html for possible solutions to that.
Hope it helps
Stefan

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NewerTech I assume kit.
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How diagnose the extra SATA ports on the Mac Pro (early 2008) logic board?

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