Step 2: Lay out the holes to be drilled
There are a several different ways to lay out the holes on the aluminum plate, the easiest is to transfer the holes from your current build platform. This also takes into account any minor variations in your build platform (the hole layout has changed since the early platforms) and reduces the chance of a measuring error.
If you (or your friend) has access to machine shop tools:
Clamp the aluminum plate to the build platform making sure to leave room around the holes you are going to transfer. Next, using the transfer punches, transfer the 3mm magnet holes and 5mm alignment holes. (This is the sort of thing you should have learned in "Machine Shop 101" :-)
1. Cover one side of the plate aluminum plate with tape, this is where we will make our transfer marks.
2. Firmly tape the build platform to the tape side of the plate. Use both horizontal and vertical strips and wrap them around the back. You want as little movement as possible while you make marks.
3. Using a sharp pencil (or a .3mm mechanical pencil) carefully make marks through the platform holes on to the tape below. You can either attempt to make a dot in the exact center of the hole or "color in" the hole, either way, make it as exact as possible.
Note: the magnets used by Makerbot are square but we're using circular magnets of approximately the same size. You'll be drilling into the center of the square you transferred
Either set of tools:
If you're using a bolt-on acrylic plate, transfer holes for this as well (probably 4mm, but verify with your specific platform). Note the orientation of the acrylic plate relative to the alignment holes -- you want the plate holes on the left and right side of the platform as you're looking at the Cupcake from the front. If the holes are on the front and back they will interfere with the x-travel of the build platform.