Yes, all the ball ends have one side slightly bigger than the other. Look carefully/closely and you'll see the bigger side.
I cut the brake pads as to avoid the holes. You don't have to cut them in a perfect semi circle as shown in the manual, but try to avoid the holes. Also, be sure to glue the brake caliper pins into the right bulkhead- this is a precautionary measure.
Go to Harbor Freight tools, they have digital calipers for cheap. No need to get one larger than 100mm's or so.