All pieces pictured are cut from 1/8" acrylic. The parts look sweet but I would probably recommend using 1/8" plywood for all the pieces except the build surface itself to reduce weight. The throwie magnets we use are 1/8" thick and 1/2" in diameter but this design can easily be modified to accommodate other magnets. I wouldn't suggest anything stronger, simply because stronger magnets may add some additional load on the y-axis bearings (the rods are steel, after all).

As you can see from the pictures, the 3 smaller layers replace the 1/4" thick wood piece that holds the magnets on the y-axis. If you've got an older MakerBot (batch 4 or older I think) this piece my be 1/8" thick and you'll need to make some modifications to the design to get it to work. The 16mm M3 bolts won't make it all the way to the t-slot nut in the two pieces that house the bearings either, so you'll need to replace these with 20mm long M3 bolts (though I operated my bot fine without replacing these bolts with longer ones for a bit while the bolts were on order with no issues).