Mine does something that sounds similar to what you're talking about.

Mine does it when using the engine to brake the vehicle. To prevent it, give it a little gas as you hit the clutch. Or just press the clutch more slowly. Either method will result in a smoother transition to unloading the drive-line

When I back out my driveway (up hill) and stop before backing into the street, if I just hit the clutch, I will hear thud and a noise that I'd say could come from slack in the driveline.

I'm not too worried about it. It could just be a little "give" in the tranny mounts causing the thud. And the metal to metal sound likely is just coming from the gears inside the tranny going from being loaded to unloaded and releasing a little "play" in the driveline.

I've already had the tranny rebuilt to fix the "popping out of first gear" problem and it did this before, and it still does it now. For as sloppy as the manual tranny is in this car, I'd consider it normal.