2009 Mac Pro boot issues

I am working on a 2009 Mac Pro with El Capitan 10.11.3.
The problem is that the system which is now on an SSD will only boot up when connected to a USB port. When I connect it to the motherboard, nothing happens. Also a HDD which has the same El Capitan on it will spin up but the system does not boot up.
When the SSD is connected to a USB port the system boots up but will not recognize any physical HDD or SSD connected to any of the 4 SATA connectors on the motherboard.

When booted up via USB, the LEDs for SYS PG, EFI DONE GPU OK are lit green. The LEDS above these for PSU PRWON and 5V STBY are lit but I believe that the 5V STBY was orange in color. The PSU PWRON is green. Today is 2/29/16 and I will not have access to the computer again until 3/2/16.

I have not checked any voltages yet with a meter. Troubleshooting ideas needed, please.

Please do not double post the same thread. Your duplicate thread has been removed.

And this is a Mac Pro and not a MacBook Pro? Just get an Icy Dock tray or similar, mount the SSD in that and slide it into Bay One.

harryb2448 said:

And this is a Mac Pro and not a MacBook Pro? Just get an Icy Dock tray or similar, mount the SSD in that and slide it into Bay One.

Click to expand...

Thank you for the reply. This is a Mac Pro. I already am using Icy Dock tray and have tried all the motherboard bays (I used the term SATA connectors); but, the system just hangs and will not read from any of the 4 bays. I have tried this with only the one SSD that has the OS on it and only the HDD that also has the OS on it. When the SSD is connected via cable to USB, I can boot into the OS just fine; but, I none of the motherboard connected (other SSD and/or HDD) drives do not show up (are not recognized). I have made sure to insert the trays correctly; but, I cannot say the same for other persons who have tried to install drives using the Icy Dock trays. I fear that something may have been shorted out and electrically damaged on the motherboard. I will check this out later this week. _jbregand

Thank you. I was surprised to see 2 postings but could not readily see how to delete one of them. I was also in a hurry because the system had timed-out on me and I was mentally losing my full train of thought. I'll work on that one._jbregand