Where was the wall?
Rashi: He saw the building of one house, north of the city, like it says explicitly at the end of the Sefer, and a wall around it.
Radak: They were starting to build the wall around Har ha'Bayis. The entire mountain is called Beis ha'Mikdash.
Vilna Gaon: It is the wall of Ezras Nashim. In Bayis Shelishi, it will surrounded the entire Bayis.
How much is "Shesh Amos ba'Amah v'Tofach"?
Targum Yonasan: Six Amos, of Amos that are an Amah and a Tefach. Rashi ? these are intermediate Amos 1 of six Tefachim ? each is an Amah of five Tefachim and an added Tefach.
Radak: It is six Amos, each of which is a Tefach more than the known Amah of five Tefachim. 'The Amah for building is of six Tefachim; the Amah of Kelim is five Tefachim' (Kelim 17:10).
Pesachim 86a: There were measuring rods in the wall of the eastern gate of Har ha'Bayis. One was six Tefachim and half a finger, and one was six Tefachim and a finger. People who supplied Hekdesh gave according to a bigger Amah, lest they shortchange Hekdesh and transgress Me'ilah.
Was the width of the building only one rod of six Amos?!
Rashi: This was the width of the wall. Malbim ? the walls of Har ha'Bayis are 500 Amos long in every direction (42:19-20).
Vilna Gaon: The wall [of Ezras Nashim] stood on a foundation six Amos wide.
What had the height of a rod of six Amos?
Rashi: The outer wall around Yerushalayim. It was low ? 'all walls were tall, except for the eastern wall, for the Kohen who burns Parah Adumah stands in Har ha'Mishchah [and sees into the Mikdash]' (Midos 2:4). Radak ? in some ways, Olei Bavel built Bayis Sheni like the form of the Bayis in Yechezkel,. Even though the verse implies that the entire wall was low (only the eastern wall was low).
Vilna Gaon: The foundation of the wall [of Ezras Nashim].
Malbim: "Saviv Saviv" teaches that the wall was six tall in every direction (unlike Bayis Sheni ? PF).