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UPDATE

I'm not sure the below is correct. I think there is a problem with the link negoatiation between 1.5 (sata), 3.0 (sata2) and 6.0 (sata3). Something isn't jiving. You can see this post where people more interested in this than I am located a tool to change the speed: http://forums.macrumors.com/showthread.php?t=1584023&page=2

After I upgraded a client's Macbook Pro (Mid 2009) 250GB hard drive to a 1TB WD WD10JPVT and cloned it with CCC, the Macbook Pro was sloooooowwwwww.

Being beachballed to death, I searched for a solution. It's technical but basically the SOFTWARE UPDATE in OSX upgrades the EFI FIRMWARE to v1.7. I don't know why exactly but downgrading to EFI FIRMWARE to v1.6 fixes it (shamelessly reprinted from the Crucial forms).

Verify you have a higher version number than 1.6.

1. -click APPLE > ABOUT THIS MAC > MORE INFO
2. -find "Boot ROM Version"
3. -it should say: MBP53.00AC.B03
4. -download http://hotfile.com/dl/109001076/5dfaf39/aluminum.macbook.pro.recovery.dmg.html
5. -open DiskUtility and drag the above image to the left.
6. -plug-in any USB flash drive (no need for large capacity).
7. -click the USB from the left and erase with "Mac OS Extended (Journaled)".
8. -click the image and choose the RESTORE tab.
9. -in the destination drag the USB drive.
10. -click restore.
11. -beboot while holding the option key to select the USB drive from boot menu.
12. -the Apple logo will come up and a dark gray bar will start to move right under it.
13. -sit relax and wait for the process to be done.
14. -Macbook Pro will reboot automatically.
15. -now open System Information and make sure that Boot ROM Version is MBP53.00AC.B02.

If you get "Could not find any scan information. The source image needs to be imagescanned before it can be restored."
-click on the image file in the list on the left.
-click on IMAGE > SCAN IMAGE (in the menu at the top).

The final fix for this is to change the SPECIFIC hd cable, with a 2010 FOXCONN model hd cable that is designed for the faster controller. It's a 15 minute fix and you should be running EFI Firmware v1.7 without any issues.
Here are the details:

PART#:
922-9314

iFixit part no:
161-061-1

FOXCONN#:
50 12. 02 6

APPLE part#:
821-0989-A (NOT part#: 821-0812-A)