You could still be looking at a hardware failure situation here. I have seen hard drives with absolutely perfect SMART attributes pass all the tests but still show the classic signs of a hard drive beginning to fail. A significant slowdown is one of those signs.
What I would suggest is that you find some way to observe the hard drive over a long period of time at considerable load. If there is a problem, eventually it will show up in the SMART attributes. It's not an ideal solution, and your problem may not be hardware failure, but it would be a good idea to rule that out before pursuing any other diagnostic methodologies.
