Hi Jake,
I am most interested in your post since you seem to have indentified the "bugs" as harpacticoid copepods. This was my first guess as well, though I am by no means a copepod specialist. (See my comments first page of this thread)
I had posted some fairly good pics of some of the appendages of the bug and also speculated that perhaps the primary damage was done by the larval form of the animal. Dr Ron replied saying that a "reality check" was in order. He said in rather certain terms that the animals are amphipods and gave some examples of the relative anatomical differences in amphipod vs copepod. I guess I'm a skeptic and didn't buy everything he said, but some comments were pretty hard to argue. (I saw a single eye spot with three distinct reflecting regions, he saw two separate eyes. I thought I saw caudul rami, he saw a "fan tail" We both did see what appear to be oostegites. I now have a few better images of this particular appendage. It appears to be the last appendage on the animal and could be described as a leg with a modified flat disc in it. The animals are definitely using this appendage to hold an egg sac. I have not been able to observe any developing larvae within the space between the wide spots, which Dr Ron called the brood chamber.) I believe the text of this thread is in the coral forum.
Anyway, now you are saying they are copepods so I am curious as to who has made the correct ID. It would be great if you could get your expert contact to elaborate on his ID and the characteristics he used to make the ID!
As for what I have seen, since making those posts some back, I do have a little more to add. I have observed the bugs crawling down into the polyp's openings and then back out. The coral did NOT eat the bug but instead was irritated by the bug's presence. I have also seen what appear to be very small younger versions of the bugs on the corals as well. Unfortuantely, I don't have a micrscope capable of sufficient resolution to get a good photo. I have one or two photos of the red eye spot showing the three reflective areas, but I suppose this could be an early naupliar eye before developing into two separate eyes. I also have several pics of the bugs using their largest forward appendage to grasp the coral and this appears to be how they hold fast most of the time. It does not seem to difficult to think many of these bugs crawing around all over the coral could create quite a bit of irritation.
Given your copepod contact and your assimilation of data on these animals, it would also be great if you post your findings and the compiled observations. Though I understand it will be VERY difficult to separate real observations from percieved observations.
Keep us posted, Mutagen