Picking up on one point:
"Amaral being made arguido... Was years after the event, you have to ask why"
The PT legal system may sometimes appear to work in mysterious ways, but surely not to the point of making the coordinator of an investigation an arguido over one case overnight due to the fact that a different child had gone missing a few hours earlier... yet kept him on the case.
It might keep the [ censored word ]s happy, but I doubt that it was more than a coincidence.
As an example: A police disciplinary investigation was conducted into Cristovão in 2005 over the Cipriano case, which resulted in 120 days suspension... which he appealed and the yoyo went on, but it wasn't until 2012 that an official notice was published rejecting his appeal.
http://www.tvi24.iol.pt/sociedade/paulo-pereira-cristovao/ministra-nega-recurso-a-pereira-cristovao-de-pena-aplicada-pela-pj
The Portuguese system was simply slow. The numerous changes that have taken place are attempts to speed it up.
The investigation into the allegation of covering up the torture of Leonor Cipriano may not have come to fruition for "many years after the event" but as you have succinctly explained that was because of the slowness of the justice system and nothing else.
Any notion that there may have been a connection between Mr Amaral's arguido status declared on the 4th May and his subsequent trial finding him guilty of perjury has any connection to Madeleine McCann's case is risible.
Being made an arguido in
any case involving accusation of torture of a prisoner should perhaps have occasioned his removal from active duty until the case was resolved.
The fact the case being brought against him was of covering for officers under his command who stood accused of the torture of a missing child's mother should have been enough to have had him replaced as co-ordinator of Madeleine's case.