You very well may have gotten the wrong one. I know that there are also two available for the 96-00 model Civics as well, but I do not know which one is correct. I saw this when my friend bought his. One matched perfect, and the other was off slightly.

Like MaxBoosT said, the MSD caps are for use with the MSD ignition boxes and external coil systems. You will probably not be able to get just the cap to work without at least buying and installing an external ignition box.