To which goat is the Pasuk referring?
Rashi (from Zevachim 101b): It is referring to the goat of Musaf Rosh Chodesh.
Targum Yonasan: All three Chatas goats (also of the Mi'lu'im and of Nachshon) were burned, but Moshe asked only about Chatas Rosh Chodesh. 1
Peirush Yonasan: Some explain the Targum like this, like R. Nechemyah (Toras Kohanim 1:2:8), that it was burned due to Aninus; if so, all three were burned; (Hashem permitted eating the Minchah in Aninus, but not other Kodshei Sha'ah. (PF) Rashi (refer to 10:16:151:1) explains why Moshe asked only about Se'ir Rosh Chodesh.) Others explain the Targum 'all three of them', i.e. Aharon and his sons, burned Se'ir Rosh Chodesh.
Why was it burned?
Rashi #1: Because it became Tamei. 1
Rashi #2: Because Aharon and his sons were Onenim (no one could eat it in the permitted time).
Rashi (19): This opinion holds that if it were Tahor, they could have eaten it at night, for Aninus Laylah is Mutar Min ha'Torah. See also Ramban. Da'as Zekenim - why was it burned? Korbanos Tzibur are offered [even] b'Tum'ah! (I do not understand his difficulty. They are offered b'Tum'ah, but not eaten b'Tum'ah, except for Korban Pesach! - PF)
What is the significance of the double expression "Darosh Dorash Moshe"?
Rashi (from Toras Kohanim): Moshe wanted to know why the one was burned and why the others were not eaten.
Our text of Toras Kohanim: Moshe wanted to know why the one was burned and why the others were 1 eaten.
Moshav Zekenim: This is difficult. Moshe commanded to eat them. If so, he had only one question!
Why did Moshe address Elazar and Isamar, and not Aharon?
Rashi: In deference to Aharon he turned towards his sons and vented his anger. 1
Even though in fact, all three had burned the Chatas (according to one Perush of Targum Yonason), so he was equally angry with Aharon (EC).
Why does the Pasuk add the word "Leimor"?
Rashi writes that the verse refers to the goat of Musaf Rosh Chodesh. Perhaps it is the Chatas of the Mi'lu'im, or of Nachshon!
Rashbam: The Chatas of the Mi'lu'im and that of Nachshon, were both eaten.
According to the opinion that it was burned due to Aninus (no one could eat it), it cannot refer to the others, which were Kodshei Sha'ah. It was permitted to eat them in Aninus! (This is unlike one Perush of Targum Yonason - refer to 10:6:1:2*. - PF)
Even though that verse discusses Musaf of Pesach, R. Yehudah (the author of a Stam Sifra) equates the Chata'os of Rosh Chodesh and the Regalim (Shavu'os 2a. - PF)
Sifsei Chachamim: It says about Korban ha'Am (including Chatas ha'Milu'im) "v'Chaper Ba'adam" (9:7)! That is not true Kaparah, rather, mere cleansing and Hechsher. (Our texts of Sifsei Chachamim say "Ba'adcha". Surely this is a printing mistake; that refers to the Egel Chatas of Aharon! - PF)
Kidushin 30a says that the middle words of the Torah are "Darosh Dorash." What is the significance of this?
Moshav Zekenim: Darosh is in the first half, and Dorash in the latter half. 1 Even though the generations before you expounded reasons and secrets of Torah, also you should expound, and receive reward! "Salseleha u'Sromemeka" (Mishlei 4:8).
They are far from the middle! Daf Al ha'Daf (citing R. Y. Alter) - it is the middle pair of doubled words. Chofan Aharon - it is the middle of 89 such pairs of words with the same root, e.g. Remes ha'Romes; if the roots are different, e.g. Lech Lecha, it is not counted, even if they are spelled the same.