I propose some changes here too:
3.Inland
"São Paulo",
"São Salvador do Congo",
"Cidade de Minas",(shouldn't this be part of the brazilian post-independence period? Yes i confused this city with Ouro Preto, both were the capital of the same state in diferrent periods )
"Ouro Preto", (added)
"Tete", (#Moçambique)
"Huambo", (added; #Angola)
"Diamantina",
"Vila Rica",
"Belém",
"Cuiabá"
"Manaus" (might be considered part of the brazilian period) Yeah, probably, just was trying to represent the Portuguese presence in the Amazon River,
"Goias", (I don't know if it should be included)Yeah you are right
"Oerias", (you menat Oeiras? doesn't seem important enough)It was the capital of a state in the middle of Colonial Brazil
"Alpargatas", (??? where is this?)An old city in the Northeast region, i found in an old map here at home =P can't be very trustworthy
4.Coastal
"Ponta Delgada",
"Funchal",
"Goa" (conquered, but the city was effectively re-founded),
"Angra do Heroísmo", (added)
"Luanda",
"Porto Seguro",
"Rio de Janeiro",
"Macau", (added)
"Moçambique" (island of), (added)
"São Jorge da Mina", (added)
"Recife", (added)
"Olinda", (added)
"Benguela", (added, #Angola)
"Lourenço Marques",
"Quelimane", (added; #Moçambique)
"Díli",
"Bissau", (added; #Guiné-Bissau)
"Arguim", (added; #Mauretania)
"Vitória", (better remove this one, not important enough)
"Rio Grande de São Pedro", (better remove this one, not important enough) Wanted a city to represent the Portuguese settlement of the pampa in south brazil, and this was an important port in the period.
"Desterro", (??? I don't think this belongs here; neither did Brasilia, in the original list) Better take out this one