What I've read so far, mainly Luz Soriano, and regarding the area of Leiria, focus is given to the sanitary problems after the passage of the French.
Most parishes report hunger, which is considered the massive cause of death. They also report large numbers of bodies inside houses everywhere, with the problem of burials being put, because there was no space in the churches (cemiteries would only become the norm in the 1830's).
Epidemics was the next big problem, mainly because of the unburied bodies, not only humans, but also horses and other such beasts, mostly on the French service and put down. The few inhabitants of Leiria (the most important city of that part of Estremadura) were shortly after afected by an epidemics of Cholera.
Another problem was the hordes of orphans roaming the country.
Last but not least, and as usual in such situations, there was a big problem with criminals. Some mention Spanish desertors, but mainly Portuguese.

As we all know, the French army were highly dependant on what the places they passed by would give them. That was one of the fundamentals Wellington had in mind for the defense of Portugal. So, most accounts I've read indicate that the MO of the French would be to approach villages, pillage whatever possible (there are mentions that civilians were tortured in order to show were the food was buried, defiant although of the previous orders from the Portuguese government to burn everything), would burn several houses and then go on to the next place.

I'll keep on looking for info on Porto de Mós, but in general, having also read the Narrative of the Campaigns of the Loyal Lusitanian Legion, by Mayne and Lillie, the situation in Porto de Mós would have been extra terryfing.

One speculation I would like to express: the French always checked the churches for gold, silver, firewood, etc., they would know people were inside as they would most probably ramsack the whole place.

Jorge