In '88, you could have Francisco Antonio stay away from wherever it was that he caught smallpox. He's more liberal than his younger brother Joao who ended up king. Have him strengthen the military so that when the war of the oranges roll around, Portugal resists enough that it becomes a lengthier war and Portugal gets over run and the court gets transferred to Brazil in '01 instead of '07. England is looking for peace at this time, so OTL they abandoned Portugal (who OTL got lucky that Godoy was satisfied with an easy victory and pressed for minimal claims). At this point, ATL, FA recognizes Portugal is the past, Brazil is the future, so he proclaims Brazil the center of the empire, reduces Portugal to a satelite powerless kingdom with Joao as king, toadying to the French (with territorial losses to Spain, and indemnity to France). This does two things: first, it permanently separates Portugal and Brazil, and second, it closes off Portugal to the English, which was Frances aim when pushing Spain to start the war (and which was achieved OTL). England goes along with this arrangement with the proviso that the Brazilian markets are directly opened to them.
This is before the 1807 push by England to close off the slave trade, so they go along with the colonies going with Brazil. Plus, in 1801/1802, they're pushing hard for a peace with France, which is why they didn't use the opportunity to open another warfront OTL, so they're more amenable to a lot of stuff they wouldn't agree to later on in OTL.
This also shakes up the Iberian penninsula OTL timeline. Napoleon used the 1807 invasion of Portugal as cover to take over Spain. Speed things up to a point where he's also looking for a peace, you take that away. No penninsular war in 1808 completely changes the south american wars of independence, and has an immense effect on European theatre. without France preoccupied in Spain, does Austria attack in 1809? with the experienced French army (tied down in Spain OTL), does Napoleon fare better in Russia? As someone said, make France more successful, and England less successful, and Brazil's fortune rises. Simply having a King who would be proactive in arranging a permanent solution for the relationship of Brazil and Portugal rather than the reactive policies of Joao changes everything.