On the right side (not sure what cylinder # it is) I found the coil was loose enough to cause this condition. How much of the rubber boot should be sticking above the head, and what can I use to firmly seat it back into place? I can just about access it by removing the right side fairing.

 

I don't remember. I just know I push them on far enough that I think I will break it if I push further. Then I give it a little tug to make sure they don't come back off.