Hello Glenn,
Ok, yes if the head is off, clean all the holes out. compressed air works fine. You can also fish a lot of crud out with a flat screwdriver or such. I always run the correct metric tap in and out of the headbolt holes before assembly to clean any thing out and then used compressed air again. If you do not have a tap you can cut a few vertical slots in the threads an old head bolt and use it to clean the threads up.This will also allow and grease or oil to escape past the bolt. The modified head bolt is only a tool and should not be used during final assembly. Never allow the bolt to bottom out at the bottom of the hole under a lot of pressure or you could damage something. My experience is that any light oil left at the bottom of the hole does have enough room to escape past the threads. Heavier grease, grime or crud could cause issues. Nice clean threads will make toque readings more accurate. During final assembly on a newly rebuilt engine, I coat the threads and rubbing surfaces at the bolt shoulder with a little graphite oil (as per early MB factory shop manuals). Even just plain oil is better than nothing at all.