I have scoured the internet for this point of Portugal's history but I can only find reference to the Peninsular War and what the armed forces were doing.
Was the there a steward? Or was it left to a few courtiers/lords left behind?
I know their army was pretty much put under the command of the British but who was there to sanction these kind of actions and surely someone worked closely with the British in Lisbon?
This is a rather detailed add on question but where would this de facto government be based? In the royal palace?
Portugal was administered by the "Governo de Regência", created by D. João just before the court was transferred to Brazil (November 26th, 1807).
The first formation ruled until February the 1rst, when Junot extinguished it. Its formation was:
After the French were expelled, in September of the same year, the Governo de Regência was formed again, this time with the following composition:
The Governo de Regência ruled until 1820, when it was dissolved and substituted by a Provisional Government.
Despite that, it's well accepted that Lord Beresford, formaly in command of the Army, was the de fact regent of Portugal during this period.