As for the valve cover replacement procedure, if you private message me with an e-mail address that can accept PDF attachments, I can send you the procedure from the service manual. It will be for a 2002 V8, but should be very similar to your 2000.
As for the clunking noise, can you describe it better? Is it a clunk, is it a rattle, is it a squeak? I would not expect it to be a timing issue, but rather a u-joint in the driveshaft, rear constant velocity joint, or something in the transmission. However, without knowing more than that it's a "strange noise" I cannot elaborate any more.
-Rod