Margaret,
Thank you for the kind words. I would have liked to have contributed further but, unfortunately, was not able to coordinate obtaining an offer from a university to undertake, and securing funding to support, a PhD. Perhaps when I retire in just a few years
Of course, as you well know from your own research, Napoleon was actively intervening in Portuguese politics even before the arrive of Junot.
"After becoming first consul, and increasingly on becoming emperor in 1804, Napoleon, intent on depriving Britain of her continental markets, and exploiting his continuing alliance with Spain, sought closure of the remaining ports of the Iberian coastline. Portugal’s resistance to Napoleon’s demands was met with an increasingly aggressive diplomacy with the aim of depriving Britain of her continental markets. The alliance with Spain closed her ports to British shipping and exports and, with the support of Portugal, the remainder would follow. Portugal’s resistance to Napoleon’s demands was met with the dispatch of two military ambassadors – first Lannes, and then Junot, to the Portuguese court. The aim of this increasingly bellicose foreign policy was to force Portugal’s hand. Indeed, one of the effects of diplomatic pressures exerted on Portuguese ambassadors in France and the activities of these two French sabreurs was to isolate and eventually eliminate leading lights within the partido inglês, and therefore British influence on policy at the Portuguese court, and install ministers more amenable to French influence."
Anthony Gray, French Invasions of Portugal 1807-1811: rebellion, reaction and resistance, MA by Research, University of York, Department of History, Centre for Eighteenth Century Studies, June 2011, pp. 44-45. Junot's imposition of the French military council is covered on pp. 62-63.
http://etheses.whiterose.ac.uk/2569/1/MA_Thesis_The_French_Invasions_of_Portugal_1807-1811_Online_Version.pdf