The PC/104 specification outlines key locations for connector positions B10 and C19 (see Appendix B of the PC/104 specification version 2.3). This requires that these connector pins be removed and their corresponding sockets be blocked. It would be ideal if everyone followed the specification because it prevents mis-alignemnt when plugging modules together however, as you have probably discovered, not everyone does. The plugs that we install can be removed by pulling them out of the connector socket. Usually something sharp like a pin or an exacto knife can be used for this task. The missing pins are electrically isolated (no connect) from the module so the break in continuity of the PC/104 connetor bus is of no consequence.