I just yesterday replaced both boots on my 94...  I can't imagine any noise
coming from a rubber boot.
What do you mean ' as the rubber hyperextends ' ???
The narrow part of the boot should be slid down (using appropriate
lubricant) over the shifter so that it is pretty much at the same level as
the base of the boot.  If it is installed this way, the throw of the shifter
does not move the rubber much at all.  If the narrow part of the boot is
still high up on the shifter,  then it might stretch the rubber boot when
you are in gear.
It is easy enough to remove the center console to see what is making the
noise.

Pete

you can buy some "quitenizer" spray at Auto zone :)

The boot shouldn't clunk.  Remove the boot and check to see that the bolts
holding the shifter in place have not come loose.