Sorry, it's hard to be descriptive without really seeing.
Are the #2 & #4 mains drilled straight through from one side to the other, as in "I can see straight through the crank."?
Next question is are #2 & #4 mains drilled twice(hole every 90 degrees) or once (hole every 180 degrees)?
From what I can see in the pics, the holes are only drilled once, and are what I would consider "out of time" with the crank throws. This is mot likely why the mains are half grooved. You would probably be best off drilling the holes in the correct timed position, and plugging the holes as mr p described.