פירוש על סוכה 3:6

עלתה חזזית – like thin blains/pustules.

If a rash spread out on a majority of it, or if its pitom is removed, if it is peeled, split, or perforated so that any part is missing, it is invalid.
If a rash spread out on a lesser part of it, if its stem was missing, or if it is perforated but no part of it is missing, it is valid.
An etrog [which is black] as an Ethiopian is invalid.
An etrog which is green as a leek: Rabbi Meir declares it valid And Rabbi Judah declares it invalid.
The Torah says calls an etrog “the beautiful fruit of the tree” or “the fruit of the beautiful tree.” Due to the mention of the word “beautiful (hadar)" the rabbis were more demanding regarding the physical perfection of the etrog than of the other three species. Indeed, to this day people are very concerned that they should have a beautiful “mehudar” etrog. An extreme example of this is the man who paid one thousand dollars for an etrog in the movie “Ushpizin,” a movie which I recommend.
Sections one and two: If there is a rash, which might refer to some discoloration, or things like warts (not just bumps, which are considered desirable in an etrog) on a majority of the etrog, than it is invalid. The pitom is the funny looking mushroom which sticks out of the ends of some etrogim (Google pitom and etrog and you can find some nice pictures). I should note that not all etrogim have a pitom. An etrog without a pitom is valid, indeed in some ways it is preferable because it is less likely to become invalid. The etrog is invalid only if the pitom was there and was then removed. However, if its stem, the part of it which attached it to the tree is removed, it is still valid. The stem is basically not part of the etrog.
Likewise it is invalid if it is peeled, split or any part of it is missing.
Section three: A black etrog is invalid.
Section four: There is a debate over the green etrog, Rabbi Meir declaring it valid and Rabbi Judah invalidating it. In Israel one sees many green etrogim, which never fails to surprise my family (as does the pitom-less etrog).

על רובו – it is one place, for we require the majority, but in two or three places, even on the minority, it is invalid. And on its pestle-like protuberance on the blossom-end (i.e., of the Etrog/citron), even a little bit is invalid, for it appears there more than in the rest of the places.

פטמתו – the beauty at its head, like the protuberance on the blossom end of the pomegranate.

נקלף פסול – and specifically if was completely peeled off, but it is valid if only part of it [was peeled off]. And there are those who say the opposite – that if part of it was peeled off, it is invalid, for it appears like it is striped/speckled, but if it is completely peeled off, it is valid. But that being peeled off is not that the peeling was removed until the whiteness that is in it appears, for this is lacking and invalid, but rather, that a thin crust/coating was peeled off from it and its appearance is green as at the beginning.

ניקב – a perforated hole from side to side, even of a little bit of it is invalid, but if it is not perforated, and is not missing anything, such as when he inserts a thick peg/nail , if the puncture is as wide as an Issar, it is invalid; less than this it is valid. And this puncture which is not missing a little bit is valid, as we teach further on that which is not perforated and is not as wide as an Issar.

אתרוג הכושי – that grew here and is black is invalid. But, a Cushite/dark-colored Etrog that grew in the land of Cush, which is its manner and is valid.

ורבי יהודה פוסל – And the Halakha is according to Rabbi Yehuda. And all of these are invalid on the First Day of the Festival [of Sukkot]., but on the Second Day of the Festival with the rest of the days, everything is valid.