Federation Commander

The Ion Pulse Generator in Jamming Mode (5R4a) is used at the end of the Defensive Fire Step. Do I understand this to mean that the Vudar player decides to use his/her IPG as a Jammer BEFORE any of the players decide what they will fire or even IF they will fire weapons?

That is correct. The intent is to convince your opponent to not take the shot at all, or suffer a penalty for taking it. The decision point is deliberate.