Hi, these are my comments regarding your questions, I hope I can help you:
1. What are the dimensions of the header pins? Can you confirm they are 20mm tall?
I would guess you used a taller header pin so that you can use the same height spacers between the Due and shield, and shield and cover
I have found 3 pin headers which are suitable for the job, you can see them in the image below:
The most important part is the length of the "long pin" (distance between the black insulator and the end of the long pin): less than 11mm will place the two boards too close (I think that 10mm could also work). 11-12mm is a very good length (pin headers A and .
Using a longer pin like the C, which is 16.5 will work perfectly but the boards will be a bit more separated.
Any of the A, B or C will do the job, but A or B make the pedal more compact. I haven't been able to find them in Mouser nor Farnell, If somebody found any nice pin header online please post it!
2. What length spacers do you use? Also, are the spacers responsible for handling the forces of stomping on the pedal button, or is the job of the screws?
I use a flexible plastic tube which can allocate a 3mm bolt inside and is 6mm diameter. I just cut it to the desired length with a scissors depending on the pin header.
The stomping forces are handled by these spacers. Fortunately the pin headers keep both boards pretty tight and just a little help is needed. I don't use any spacers in my pedalSHIELD (because I assemble/disassemble it almost every day) and I don't miss them, so they are not mandatory.
3. What length of the screws did you use?
M3x40: Metric 3 bolts, the best length is 40mm cause you can use it with almost any pin header (It works with the previous mentioned A, B and C).
4. And last, have you thought of designing a permanent enclosure for the pedal?
I wonder if we could take a cheaper pedal and cannibalize it for the case?
When I first designed the PCB I did it to keep the same size as Arduino DUE. The classic aluminium Hammond enclosures used for DIY pedals 1590A and 1590B are too small. 1590BB looks too big but maybe using switchcraft jacks could work, but I did not checked that yet.
It fits nice in a "bimbox 5004-14" 120x40x65 aluminium enclosure I found in a physical electronic store, maybe in a local store you can find a case which fits good.