What sort of distinction is the Torah warning about?
Rashi: A distinction between cutting the majority of the two Simanim of an animal and the one of a bird (which renders the Shechitah Kosher) and cutting exactly a half (which does not). 1
Targum Onkelos and Targum Yonasan: A distinction between Kasher species of animals and birds and non-Kasher ones.
Rashi: The difference between them is a hair's-breadth. Otherwise, a warning to draw a distinction between a cow and a donkey would be superfluous. See also Torah Temimah, note 55, who elaboratess.
What is the Torah referring to when it adds "ve'Lo Seshaktzu es Nafshoseichem ... "?
Seforno: It means that one should not render oneself disgusting oneself by eating 1 of the species that the Torah has prohibited.
Targum Yonasan: It is referring specifically to refraining from eating animals and birds that have been clawed by a wild beast or by a bird of prey.
Seforno: Specifically eating - which contaminate the soul - but not merely touching (which renders only the body Tamei). Presumably, that is what Rashi means when he comments on "le'Tamei" - 'Le'esor'.
What does 'u've'Chol asher Tirmos ha'Adamah" incorporate"?
Rashi (in Makos 16b): It incorporates all animals, beasts and birds - but not vermin that crawl on the ground. 1
Rashi (Ibid.): Which are not subject to the specific Isur in this Pasuk, because they fall under the category of 'Sheretz' and not of 'Remes' - See Rashi, Makos, 16b DH 'Tzir'ah Lokeh Sheish'.
Why does the Pasuk begin with Achilah ("ve'Lo Seshaktzu es Nafshoseichem") and end with Tum'ah ("asher Hivdalti lachem Letamei")?
Me'ilah, 16b: To teach us that the Shi'ur Malkos for eating a Sheretz is the size of a lentil, 1 just like the Shi'ur Tum'ah 2
Seforno: Because, as opposed to touching and carrying, eating forbidden foods contaminates the soul.
Having mentioned "bein ha'Beheimah ha'Tehorah la'Teme'ah", what is "ba'Beheimah u've'Of" referring to?
Targum Yonasan: It refers to an animal that has been 'trodden' by a wild beast and a bird that has been 'trodden' by a hawk, respectively.
What is "u've'Chol asher Tirmos ha'Adamah" referring to?
Rashi ( in Makos, 16b): It refers to animals, beasts and birds ? not vermn. 1
Se Rashi ERuvin, 28a, DH 'Tzir'ah Lokeh Sheish'.
The Pasuk mentions distinguishing "between the Tahor and Tamei animals", and "between the Tamei and Tahor birds." Why does it switch the order?
RS"R Hirsh: Whenever the Torah obligates distinguishing, we must ensure that the two kinds not mix. One may not be Metaher the Tamei or Metamei the Tahor, or to forbid the permitted (Yerushalmi Terumos Sof Perek 5). Also above (11:47), it switches the order like this.
Ha'amek Davar: It mentions first what the Torah listed - the Tahor animals and the Tamei birds.
Torah Temimah: Because there are more species of Tahor animals than Tamei ones but more species of Tahor birds than Tamei ones. Therefore, the Torah gives precedence to the Tahor species of animals, and the Tamei species of birds - since one tends to separate the minority from the majority. 1
As the Gemara points out in Chulin, 63b - Torah Temimah, note 58. Or, as the Oznayim la'Torah points out, due to the principle of always teaching one's Talmidim as briefly as possible, as the Gemara teaches in Pesachim, 3b.