I'm loving this story. it's something really different. The vast majority of stories focus on the united states or the three great nations of europe (france, germany and england). This is not a bad thing, but it gets repetitive after a while. The history of this portugal 2.0 is becoming one of my favorites if not the most favorite for its innovative idea.
Portugal could use Spain as a nice shield against Napoleon, I don't know how that would impact the relationship with Spain.
Now about the relationship between Rio and Lisbon we could have a certain dichotomy between "liberals" and "reactionaries". Colonies, even one as important as Brazil tend to be at the same time more and less liberal than the metropolis depending on the subject. Rio could, for example, not care about the death penalty and be the group that pushes the most for greater inclusion of pardos. Considering a large part of its generals, scientists and writers were pardos like Machado de Assis (the greatest name in Brazilian literature).
Pardo is an umbrella term for people with a mixture of skin colors, whether this miscegenation is mulatto (descendants of whites and blacks), cabocla (descendants of whites and Amerindians), cafuza (descendants of blacks and indigenous) .
One thing Boneheaded_Bookkeeper said about Portugal reigning over Brazil can be played as a sibling dispute over who gets more land. The more brazil expands in south america, the more portugal has to expand in asia. Brazil's focus on its army could be an important factor in the Napoleonic period, creating Portugal's greater dependence on Brazil to defend itself. A naval dependence of Brazil with Portugal already exist and create a greater relationship between them. A balance of power with brazil vs portugal and india could be a way to create a certain equality between the two kingdoms. This could create envy of Brazil with India fearing it would lose its prestige as the jewel of the Portuguese empire.
Another factor of Brazil in relation to its expansion and wars is its 8 or 80 attitude. Expanding wildly with the bandeirantes and spending decades trying to digest the new acquired land. It's the same in the war, being relatively courteous to the Argentine in the dispute for Uruguay. But in the Paraguayan War, during the final years of the war there was almost a systematic extermination of the Paraguayan population, until Solano Lopez was found and killed. (due to the fact that the population hid Solano or simply due to anger at the number of Brazilians killed in the war). The El Cristiano (a war trophy that is in the Patio Epitácio Pessoa of the National Historical Museum , being a Brazilian historical heritage). To this day, Brazil does not recognize this as a massacre, but something that the Paraguayans and their dictator brought about by attacking Brazil. which doesn't help the relationship with Paraguay these days ( The feeling that it's Paraguay's fault is the norm and I doubt that will change).
Now in a more positive note If Brazil becomes basically a junction of Argentina, Uruguay, Paraguay and Brazil (perhaps even Chile?) with its expansion to the south or/and an expansion to Bolivia. A lot of pressure will be put on portugal creating a very interesting and tense senario.
Perhaps a way to resolve this tension would be a Brazilian governor in Rio or perhaps further expansion in India bringing Indians into the struggle for power in the empire. A relationship with the Japanese will be something interesting to see due to the large number of Japanese people in Brazil. A Portuguese expansion in Spain will be another factor in the balance for power.