I drilled the holes too big in my IGO-W as well. What I did was fill them with JB Steel Stik, packing it in from the inside with a finger tightly pressed on the outside. Once they looked filled, I quickly tried to scrape off the uncured compound from the inside of the cap. Anything that was left got sanded out after it was cured. I then re-drilled with a smaller bit just spinning it in my fingers. Works and looks great now.
It would be pretty cool to tap one of the holes so you could block it with a screw, or have the option of leaving it open for a dual coil setup.