It is remarkably difficult to find anywhere in the world such an orchestrated attack on a detective's private and professional life simply because in his job he accused a foreign individual of concealment.
In my opinion he was targeted because he was the team leader. From the files it is easy to see that other men in the PJ contributed to the interpretation that he finally used in his book.
Much more relevant than the book were, for instance Ricardo Paiva's and others reports about the couples behaviour, but especially the Tavares the Almeida Report in Sep 2007 [
http://www.mccannpjfiles.co.uk/PJ/TAVARES_ALMEIDA.htm] which, even under Paulo Rebelo's coordination, was the basis for the observations in the Final Report & later in the Archival Report about the non clearance of the McCann.
The fact that Amaral chose to remove himself from the police, in order to be able to clarify the facts and defend his honour by writing a book. only gave the McCann the opportunity to go after him like jackals with their pack.
It's typical of predators to attack the isolated victim, and Amaral made himself the most exposed one.
However he is not the only or main target, the PJ as a whole is. See today's Mirror opinion by Lord Stevens [
http://www.mirror.co.uk/news/uk-news/lord-stevens-hunt-madeleine-mccann-3123394#ixzz2sgZmTI1D, as if the British Police never had an Operation Countryman or an Operation Tiberius. By the way, giving Princess Diana as the example how the British police interferes with ongoing investigations overseas was a shot in the foot.