Well, the part number for the nuts was the same from TR2 through TR4, so I don't think they changed. My belief is that they were always tall steel nuts; the occasional tall brass nuts are aftermarket (sold for a Chevy V8 as I recall).
Not sure about the copper plating, but I've never noticed any evidence of it. I use a copper-based anti-seize though, so maybe I wouldn't have noticed plating even if it were there.
As a side comment, it has been my experience that adding a heavy flat washer (aka "setup" washer) to the two outermost studs (the ones without the bridge piece) helps to keep the joint sealed. The lockwashers need to be replaced pretty much every time a nut is removed (apparently the heat cycling makes them lose tension). And a 'swivel' socket makes it easier to retorque the nuts occasionally, which will also help keep the joint sealed.