One methodological and one substantive point.
[I]f there is an instructive parallel between contemporary Iraq and the Central America of the 1980s, it's not El Salvador but Nicaragua.
There are some parallels between the Iraqi and Salvadoran cases. It is interesting to note that the constant refrain of the Salvadoran right during the 1980s was that the FMLN was nothing more than "5000 terrorists" with no popular base, depending entirely on outside support from Nicaragua and Cuba. During the first eight months or so of the Iraq insurgency, the official Bush administration line was that the insurgency consisted of only "5000 terrorists" without a popular base, sustained by outside support from international Jihadist networks. While such depictions were wildly wrong in both cases, equally or more important is the fact that the two insurgencies, and the historical and structural contexts, are completely incommensurate. The only thing that is similar between the two situations is the ideology and practice of the two U.S. administrations involved, the disagreement of most of the rest of the world with that ideology and practice, and the fact that in the El Salvador of the 1980s, as in Iraq today, the most powerful institution in the country was the U.S. embassy....
In El Salvador, an electoral regime became meaningful and began to play a positive role only very gradually and against the grain of the policies of the first Reagan administration. Such evolved out of the combination of (1) the work of elements of the Church, and in particular UCA's (the Jesuit-run university) Social Projection, Ignacio Martin-Baro's development of IUDOP (public opinion institute), his and (UCA head) Ignacio Elllacuria's appearances on Canal 12 television, their insistence that their could be no military victory for either side; (2) the impact on U.S. policy of the partnership between Congressional Democrats and the anti-intervention movement in the U.S. and the leverage that gave to the moderate professionals in the State Dept and AID against the Reaganauts; (3) the Reagan administration's need to compete with and try to outshine the 1984 Nicaraguan election; (4) the unraveling of Iran-Contra, leading to some defanging of the Reagan Doctrine vis-a-vis Salvador (the Reagan Doctrine, parallel to current Bush/neocons, stood for the pipedream that military defeat of Third World "Communists" would lead automatically to the emergence and success of "democracy"); (5) Oscar Arias' work; (6) the profound delegitimation of the Salvadoran military by its 1989 murder of the UCA's Jesuit leadership, and the Bush administration's bowing to that delegitimation; (7) the shocking of the right by the strength of the FMLN's 1989 offensive; (8) the gradual revival of the center-left in Salvador at the end of the 80s and the gradual recognition by both ARENA and the FMLN that they should accept a growing role for such, the latter made possible by the fall of the Soviet bloc (9) the UN's massive and sustained presence and commitment to peace negotiations and processes, and the courageous service of prominent people in various truth and reconciliation commissions, and the Bush administration's willingness to countenance all that and lend some support, including to the purging and reduction of the Salvadoran military and security apparatus. It is impossible to imagine either the first Reagan administration, or the similarly deluded current Bush administration, behaving in a parallel manner.
There are no functional equivalents to most of these things at the present moment re Iraq. And of course it took a full ten years (1984 to 1994) in Salvador to get to elections that were beginning to be what passes for free and honest, and elections continued to have low participation (35-40% of the voting age population) for another 10 years. Something that is parallel between the two cases is that in both El Salvador and Iraq, a highly centralized and militarized government had profoundly suppressed civil society, except for religious leaders and groups, who were killed if they became too political, but otherwise allowed to survive and maintain their institutions. But in Salvador the Church/the religious were split only along left/center/right lines, and the most powerful institutional presence, UCA and the Archbishop were superhumanly committed to what amounted to center-left, pro-democracy, anti-militaristic positions. In Iraq, religious leaders and groups are much more highly fragmented in much more sectarian ways(compounded by profound geographical and ethnic splits, non-existent in El Salvador), neither they nor their cadre having experience with elections or democracy; many are pro-insurgency; many are only conditionally anti-insurgency (in Salvador the cadre and leaders of Christian Democracy and Liberation Theology had a good deal of experience with elections from the 1960s and 70s). Is there any potential for Sistani to play a role parallel to Ellacuria and Martin-Baro in Salvador?
Now lets consider the parallels between Iraq and Nicaragua. In earlier times, the U.S. government had supported the regimes of authoritarian, quasi-fascist caudillos in both countries (the Somozas in Nicaragua ans Saddam Hussein in Iraq). The manner in which those regimes were overthrown, and the character and initial strength of the new regimes, were of course very different. But after that, all we have to do is flip the U.S. role and we get some striking parallels. The FSLN regime in Nicaragua, and at least some elements among its foreign partners (the Soviet bloc and Cuba), thought the Sandinista revolution could be a model for the "democratic" overthrow of traditional authoritarian regimes throughout Latin America (the liberal middle class elements of the anti-Somoza coalition thought they were achieving something else --Costa Rica). The Bush administration, sponsor of the new Iraqi government thinks the Iraqi "democratic revolution" can have a massive demonstration effect leading to the "democratization" of authoritarian regimes throughout the Middle East (Shi'a political parties and clerics think they are achieving something else -- a very different vision, with which liberals are quite uncomfortable, as liberals were uncomfortable with the Leninist version of Sandinismo). In the Nicaraguan case, Argentine, Guatemalan, and U.S. right-wing extremists were determined to prevent any such exemplary success of the Sandinista revolution and started organizing the remnants of the Somoza National Guard and security services, with some help from neighboring Honduras, to launch terrorist attacks in Nicaragua. Elements of the first Reagan administration, in the CIA and the National Security Counsel in particular, increasingly funded and helped organize those anti-Sandinista efforts. All of this bears some comparison to the outside help the Iraqi insurgency is getting from foreign Islamic jihadists and from some Baathist elements in Syria....
It seems to me likely that at least over the next few years, the new Iraqi government will duplicate many of the faults of the Sandinista government of the years after the 1984 Nicaraguan election--and probably few of its virtues. This is probably the best we can hope for. Equally likely is either full civil war and the breakup of the country, or a quasi-Leninist Shi'a theocracy. The liberal middle class and (and its U.S. sponsors), as in early ‘80s Nicaragua, left feeling that once again they've been robbed of their birthright and their country taken off on a pathological detour - except possibly for the Kurds if they are able to move toward viable autonomy.
Methdologically (and this reflects my training as a historian rather than a political scientist), I always get leery of arguments about geographically-abstracted "historical parallels or precedents," when they reach a certain level of detail. Comparisons can be illuminating at a fairly high level of abstraction, but inevitably they break down once you reach a certain degree of specificity. (Chomsky phrases this problematic nicely in an essay from the 1980s where he discusses the parallels between Central American during that decade and Vietnam 15-20 years earlier -- alas, I don't have the quote handy.) This article strikes me as perhaps crossing that line into excessive specificity. More generally, discussions of "historical precedents" seem to me useful, mainly, when they refer to the exact, local precedents of the local, specific situation. In other words, if you want to understand what's going on Iraq today, the right historical situations to examine probably aren't Vietnam or El Salvador, it's what was happening in Iraq and its neighbors over the last 50-90 years.
Substantively, the main thing that strikes me as missing from this analysis is that in all of the allegedly parallel situations (Vietnam, El Salvador, Nicaragua), the insurgents had a very significant source of external support, i.e. their Cold War sponsors. One of the things that is striking about the resilience and scope of the insurgency in Iraq is that none of these groups have a significant, large, explicit external sponsor to supply them with a steady source of money and materiel. (Yes, Osama supports Al-Zarqawi, but no one has proven this support is much more than ideological.) How long the multi-pronged insurgency can hold out without external support strikes me as a very real question. At some point, all the stockpiled explosives and weapons will start to run thin, and then what?