The archive of the Dutch representative in Portugal contains some lists of the Portuguese navy, sadly enough is at the moment just the list for 1788 available. The list is written in French.
Ships-of-the-line
Na. Sa. da Conceicao, 80 guns, built 1763 at Lisbon, 840 men
Na. Sa. de Pilar, 70 guns, built 1764 at Lisbon,700 men, name scrapped
Meduza, 70 guns, built 1786 at Lisbon, 700 men
Ns. Sa. d´Ajuda, 64 guns, built 1758 at Lisbon, 580 men
Na. Sa. Madre de Deos, 64 guns, built 1764 at Lisbon, 580 men, name scrapped
St. Joze e Merces, 64 guns, built 1761 at Lisbon, 580 men
St. Antonio e S. Joze, 64 guns, built 1762 at Baya, 580 men
Na. Sa. do bom Soceco, 64 guns, built 1765 at Lisbon, 580 men
Na. Sa. dos Prazeres, 64 guns, built 1767 at Lisbon, 580 men
St. Sebastiao, 64 guns, built 1767 at Rio, 580 men
Na. Sa. de Belem, 58 guns, built 1766 at Para, 500 men
Na. Sa. da Nazare, 40 guns, built 1766 at Porto, 450 men, name scrapped
Na. Sa. da Graca or the Phoenix, 40 guns, built 1787 at Baya, 450 men
Minerva, 40 guns, built 1788 at Lisbon, 450 men
St. Joao Baptista, 36 guns, built 1769 at Porto, 400 men
O Lisne, 34 guns, built 1779 at Lisbon, 340 men
Tritao, 40 guns, built 1783 at Lisbon, 340 men
Princeza do Brazil, 30 guns, built 1774 at Lisbon, 310 men
Golfinho, 40 guns, built 1782 at Lisbon, 310 men
Principe da Beira, built 1778 at Lisbon
A Aguia, built 1779 at Lisbon
Galgo, 20 guns, built at Londres
Corao, 20 guns, built at Londres
Uniao, 20 guns, built at Londres
Lebre, 20 guns, built at Lisbon
Source
Archive Legatie Portugal 1702-1804 no. 40 National Archive at The Hague).