The models are sized to fit in your hand. You may have to scale by a factor of 10 if you're using MakerWare, since it tends to import files in mm, not cm.
I printed without a raft, but with extra strong supports. The standard supports tended to be knocked around by the printer nozzle. Under Print Settings, go to Custom, then Supports and Bridging. Check the Supports box, then uncheck the Align Supports box.
The pair-of-pants, caps, etc are held together by 3mm (diameter) x 3mm (height) cylindrical rare earth magnets (http://www.gaussboys.com/store/index.php/magnet-shapes/cylinders/c0303.html).
The magnets should fit snugly, and I didn't need any glue. If you do, you could try using a little JB Weld epoxy just in case. I suspect that you could also use superglue. I highly recommend printing DesignByNumber's magnet insertion tools (http://www.thingiverse.com/thing:436565) to help seat the magnets into the little holes.
For the pair-of-pants and caps models, I alternated the + and – ends of magnets around the rims of the pair-of-pants. I did this in a consistent way, for example the + was always at the front and back of the pants. For the rings, the plain ones should be aligned the same alternating way on the top and bottom rims. The ones with plus/minus signs or 90 degrees should have the arrangement rotated by 90 degrees.
The Rueben H. Fleet Science Museum in San Diego made the body of the regular and bent pair of pants be +, then made all the rings -. Not sure what they did with the caps, probably made them all + too. This keeps it very simple.