I did remove both of the dogbone mounts, and then attached that ratchet strap to pull the motor back. I don't know about this hole you are talking about, but I'll take a look and see for next time.
I don't know how the Cone could burn or rub through a wire to the PCM, but I will keep an eye on it. The filter is not touching the PCM harness at all. I am more worried about the filter coming off the end of the rubber intake tube. There is no metal or plastic joint pipe. I just trimmed the intake tube seams off and slide the filter over it.