Clutch symptoms?

First, the rattle may be related to the sheetmetal cover on the bellhousing where the release arm enters. Check to see if it's loose.

Second, the thud may indicate that the clutch isn't releasing fully when depressed. The input shaft is still spinning when the gear is selected. When the synchros engage, the input shaft stops, along with the clutch disc, Because there's still some friction there, you're going to feel a thud. Check the cable adjustment. If you're still on the stock quadrant, just use your toe to pull up on the clutch pedal to actuate the automatic adjuster. Try it a few times. Make a note of the pedal free play before and after the procedure to tell if any slack was taken up.

If this doesn't do anything, you may have other issues, such as a bent or damaged release arm, bad fulcrum, bad quadrant etc.

If it's not adjusting maybe your quadrant could be broken? Could have cracked or something. My car was doing something similar to this though, and it was the throwout bearing. It got worse and worse until it would chatter unless my foot was on the pedal disengaging the clutch very slightly. I would put money on saying it's your throwout bearing. How many miles are on the clutch in the car? Is it original? Also it's good to hear that there is finally some sort of answer to the chatter from around the bellhousing. I'll have to check to see if anything is loose around there because I have been through 3 clutches and the noise has yet to subside. I ruled out everything I could think of being the solution, until that was mentioned so thank you!

Edit to the last post, I reread your post and saw what you said about the clutch. With that mileage on the stocker, I would bet it's the throwout like I said. Also I would inspect your quadrant, especially if you drive "spirited." They are prone to cracking and warping (cheap plastic).

Get up underneath there and look at your quadrant. I would bet if its making noise though its the TOB man.