You could start with some web searches, like:
americancatholic.org/News/JustWar/Iraq/
One thing I would encourage is reading Church and Papal statements in their entirety. Reports and summaries tend to be twisted by the people reporting.
It would seem save to say that both Pope John Paul II and Pope Benedict strongly disagree with the application of Just War doctrine in Iraq. And Rome took significant steps to make its position known prior to the US invasion. Of significant concern to then Cardinal Ratzinger was the distinction between a “pre-emptive” war and a “preventive” war. The latter is wholly prohibited by international law.
As far as I know, Pope John Paul never questioned the final authority of civil authority in judging the criterian in 2309, but he did make several pointed speeches noting the the binding obligations of NATO and UN membership. Pope Benedict’s prefect also has made at least one reference to the lack of a formal declaration of war from the US congress. As a citizen, that one troubles me quite a bit (as it did when I was in Vietnam 40 years ago). You may recall that 1100+ US historians wrote an open letter imploring Congress to have a debate and vote on Iraq in 2002. The letter urged no particular outcome, only a return to constitutional law.
Since the war began, neither Pope has given any evidence in a change of position. The most significant shift is that Rome has been increasingly stressing the US’s moral obligation with regards to the horrific refugee problem - which is disproportionately Christian. The Pope is reported to have directly addressed the issue with President Bush last June. The prefect has also made some comments condemning the current US policy of using Sunni war lords to establish order is specific districts. Giving them money/weapons and letting them ethnically clense their districts does bring down the violence, but the question is at what cost and for how long?
The Church’s apparent largest problem with our so called war-on-terror is our tactics. Secret prisons, indefinite detentions, torture, and the assertion of the US government that it not bound by international treaties fall into teachings subsequent to 2309, which are not subject to the opinion of civil authoirty.
Again, it is best to read the many speeches and statements in their entirety. In discussion this subject I have seen some wholly unrelated quotes twisted beyond recognition.
