ril3y,
for non-native English speakers English and English are two different languages when it comes to explaining technical details - in particular if you are an EE or not used to technical English at all and try to explain mechanical details (I say this from experience) ;)
I think I had a pretty similar idea to what pppd tried to explain but I kept quiet because I didn't know how to express myself precisely (without looking up too many words) :D Let me try:
Because you can't put the PCB directly on the metal plate (bottom layer) pppd suggested to put an extra acrylic layer with a rectangular cut-out (the dimensions of the cut-out being slightly smaller than the footprint of the PCB) right above the metal plate that would act as a spacer for the PCB - this layer should be 1/8 thick as the contacts of the headers stick out more than 1/16 from the bottom side of the PCB.
This would lead to something like this (from top to bottom):
1. acrylic cover layer with breakouts for the vertical connectors/headers and the USB connector/jack
2. acrylic layer 1 (1/8) surrounding the Bus Pirate PCB
3. acrylic layer 2 (1/8) surrounding the Bus Birate PCB
4. extra acryl layer that acts as a holding frame and spacer for the Bus Pirate PCB - with a rectangular hole/cut-out in the middle that is slightly smaller than the PCB ... allowing the sides of the PCB to rest on this frame - so the contacts on the underside of the PCB will not touch the metal plate.
5. metal base layer with threaded holes for the screws (yup, it will require longer screws)
6. rubber feet
P.S. acryl(ic) == plexiglas, PMMA
ril3y, your design is great ... we love the Bus Pirate and use it quite a bit. So we look for a "heavy duty" version of your design, toss in our ideas and I will buy one or two regardless if there will be an option with a metal plate or not. :) :)