I think Fishbert is definitely on to something here. I know everyone has been swearing up and down that it is a firmware issue, and that it only applies to the 15", trust me, i have read every page in multiple discussions about this and similar if not related issues, and have very little hair left because of it.
I have updated to 10.6.2, and applied the new 1.8 and associated firmwares, and disabled the temporary hdapm fix. installed a Western Digital 750GB. and all to no avail. I desperately ordered a replacement sata cable from
http://www.applepalace.com/apple-mac/apple-parts/macbook-pro-parts/macbook-pro-1 7-inch-early-2009/cable-hard-drive-connector-922-8920.asp
(again, this is the link for the 17" MBPro drive cable not the 15, double check to order the right one)
Installed it, (careful not to put the excessive bends that the orig had) and 3 hours later now after doing everything in my power to get my 17" MBP unibody to beachball, click, beep, and hang up in any way etc, am very happy to say that so far... my issue is resolved 100%
The cable that arrived was slightly different in regards to the markings than the orig cable, I talked to the tech at Apple Palace and he said apple just released the OEM cable to be sold to outside vendors as a replacement part not too long ago.
For reference.
http://www.flickr.com/photos/45490168@N06/4176372407/
Hopefully, even if this is unrelated will convince someone else to take the $35 plunge and start enjoying their mac again.
Thanks everyone here for adding the helpful comments.