I used to have Condrays book but I lost it. I remember some details though. The reason for the late of information on this is the Lisbon Earthquake and tsunami in 1755 which destroyed a lot of it. What does exist seem to be largely in private collections.
The Campo Maior regiment wore blue coat with red cuffs. This may have been a continuation of the bluecoats that were introduced during the Restoration War against Spain. The Marines (Terco da Armada) wore green coats with yellow cuffs and yellow stockings (at late in least 1600s the stockings were yellow). There is a painting mentioned in the book showing this marine with the hat not yet turned up (I think around 1700 but the author says it looks much earlier). In 1725 the yellow cuffs became red. Red sashes were worne by officers. The Portuguese infantry didnt introduce gaiters until some decades after the WSS (I think in fact not until 1762) . The Lisboa regiment seems to have worne light blue with white lace. The vast majority of Portuguese infantry mostly wore white-grey coats during the WSS (a colour referred to as "Alvadia" meaning "off white"). A painting from around 1720 shows a soldier of the Porto regiment wearing an off-white coat with red cuffs. The book mentions an order for alvadia coats with different facings (cuff colours) including red. The pikemen were told to train with muskets around 1703. Condray suspects that the colours of the regimental flags might give a clue to the facing colours of the regiments. These are mentioned in his book.
The book showed a sketch of a militiaman of the "Tercos Auxilios". It says: alvadia coat and cuffs, red stockings. Interestingly the man still has a bandolier like the kinds seen in the 1600s. Also the hat looks more like a broad brimmed hat turned up than a tricorne in my opinion.
The cavalry at first didn't have uniforms. An English witness during the War of the Spanish Succession mentions some wore Montero caps at this time. However from around 1708 white-grey uniforms are mentioned.
Around 1640 a Royal Halberdier guard was raised wearing green coats. During the WSS there was a Royal Guard of Archers but it was ceremonial and accompanied the king. Also wore green coats. Not entirely clear to me whether the two units are the same but may have been. Around 1728 their uniform changed to red coats I think with gold lace.
I have Manuel Ribeiro Rodrigues Book on "300 Years of the Portuguese Military" (translation of title). It shows an engraving of a parade by grenadiers and they are wearing bearskin caps with a tongue coming out of the back (similar to other armies). However the musicians are wearing mitre caps with plates of the style of late 1600s. The parade is from decades after the war though (I think around 1740). There are suggestions that its possible the mitre caps with plates were a continuation of an earlier tradition of grenadiers wearing those but in Ribeiro's book it shows a grenadier statue in Olivencia (now administered by Spain since the War of the Oranges) wearing a mitre cap. The mitre has a grenade emblem on it. The statue is thought to date from the late 17th or early 18th century.
For generals uniforms: while in this period in Europe, generals often didnt have a uniform, there is this
painting of the Duke of Cadaval from 1727. it is 13 yrs after the WSS but might still be good as guide.