Step 1: Process
Hopefully there isn't another instructable like this one but I haven't made it through the whole list yet so...
The pictures are in order matching the numbers of the instructions.
1. First remove one side of the paper cover on the plexiglass. Don't remove the paper on the other side yet.
1(alt). Don't remove the paper from either side just use a pencil and a razor to make your grid. Simply remove the square you want to expose to alteration. I didn't use this process because it works better for protecting from spray paint than the repeated abrasion of a sanding pad. If you want colored squares this is probably the way to go though. Just remember that the board will hopefully be getting use and there is a chance that the paint may eventually scratch off.
2-a. Decide how large you want the squares to be and make sure it is going to turn out to be an eight-by-eight square with square sections.
2-b. Mark the points where the lines are going to cross to create a grid as I did in the second photo. Use the ruler and grease pen to make the lines and eventually a grid. Don't remove the paper on the other side yet.
If you chose to keep the paper on both sides, this is were you would use a razor and the ruler to cut the squares you drew.
3. Adhere a line of tape on either side of one row and cover every other quadrant using the lines to keep relatively even squares. If anyone knows of a better way to frost plexiglass don't hesitate to comment but I used the scoring pads to lightly sand the unprotected squares. Repeat the process for every row and it should take about 2 hours to complete. Don't remove the paper on the other side yet.
4. Use the file and the ruler to make the trasition between frosted and clear squares more defined. Use the tip of the file to scratch a groove in the surface on the edge of the squares. Be really careful here, moving too fast will probably get you a nice blemish across half the board. *sigh*
Don't remove the paper on the other side yet.
5. If you want to put the board on stands to keep it elevated and protect the underside from scratches, or you want to make a three level board... read step five, otherwise move to step six.
This is the most dangerous part and I probably should have mentioned it before but, if you don't really care if it turns out perfectly symmetrical do this before you put all the effort into making the board. Okay, using the grease pen mark where you will be making the holes. For the three-tier board I drew diagonals from the edge of the grid to the edge of the plexiglass.
I've heard water is better for drilling plexiglass but I used olive oil. In order to keep the glass from cracking place it on a hard surface (that you can put a hole or two in), use only the weight of the drill to press down, use every graduation of bit you have to reduce the stress and lubricate and clear the bit between holes.
6. Now you can remove the paper from the other side of the plexiglass. Make sure there isn't any of your lubricant on the area to be glued. Flatten the spikes on the thread plugs (or get the kind without spikes... they're more expensive... by 5 cents) and place some 2-part epoxy on the shaft of the plugs. For aesthetic reasons turn the board over so the smooth, un-scored side will be facing up after you glue in the plugs. It makes it nicer to play on a glassy-smooth surface. Place the plugs in the holes and let them dry for however long the glue recommends.
Voila! The board should be complete and, after you clean off the fingerprints, it should look fairly nice.
The last picture is what the three-tier board ended up looking like... and yes I have played 3D chess with rules that account for it nicely. Thank you for reading my first instructable, I hope everything works out if you try it. Also, I realize that there are other mods of this and I will try to address them if you send me a message or make a post but I will add only those that retain the base concept.