The leather shift boot is available from Pep Boys for $25-$30 (Although I have seen similar ones for less elsewhere after-the-fact). Its a replacement manual shiftboot with an elastic at the bottom.

The steps are roughly as follows:
  1. Remove shifter handle (remove the staple in the front, then pull up)
  2. Remove the top part of console (there are two screws hidden under the coin tray in the center glovebox, i think it just comes up after that -- i dont remember)
  3. Remove sliding mechanism from underside of console (its white with black sliders.)
  4. Remove black plastic sliding peices from sliding mechanism.
  5. Push the shift boot throught the console hole and secure it by sandwiching it in place with the sliding mechanism. Test fit the boot and trim as needed (the boot is longer that needed). You may want to temporariy hold the shift boot in place using some tape to free up your hands to reattach the sliding mechanism.
  6. Put everything back together, without the black sliding pieces.

Note:
During reasembly, make sure shifter rod goes thought the loop/hole
in the middle of the sliding mechanism. Otherwise the sliding mechanism
wont work properly. The current gear wont be shown and some gears may be
locked out because the mechanism may be in the way. Also, dont tighten
the screws in the sliding mechanism too much. This could make its
operation stiff and possibly cause damage.