All I've seen regarding the Cutty Sark in her Portuguese schoolship days are a few photos and some brief notations in the standard histories of her - which you've probably already looked at. As I recall she was, at least for part of her Portuguese career, painted with phony gunports.
I used to have a copy of a fascinating article called "The Restoration of the Cutty Sark," by Frank G.G. Carr, the gentleman who was in charge of the project (back in the 1950s). I bought it in the ship's gift shop in 1978, and apparently lost it in one of the four changes of residence I've made since then; I've ransacked the house looking for it, but can't find it. As I remember, though, the restoration project didn't entail any major changes to the deck furniture. (The money for such things wouldn't have been available.) That implies that the Portuguese left such things as the deckhouses, cargo winches, windlass, etc. pretty much as they found them. (Sometime or other she got a new steering wheel; I don't remember the details of that story.)
As I recall, the most conspicuous change the Portuguese made (other than the cutting down of the rig) was the conversion of the 'tweendecks space from cargo hold to living quarters for the ship's cadet complement. That entailed, among other things, the cutting of a row of round portholes on each side of the ship. Mr. Carr's restoration team considered removing those ports, but eventually decided to leave them where they were as a means of providing air circulation to the ship's interior. The alternative would have been to install an electric ventilation system, with the attendant ductwork and decidedly unauthentic noise of blowers (and a good deal of initial and ongoing expense).
The Cutty Sark is currently confronting a huge restoration and repair project. I believe there are plans to replank the hull - and do away with the portholes.
I'm afraid I haven't helped much; that's what I can remember.
Youth, talent, hard work, and enthusiasm are no match for old age and treachery.