I am now going to write a new way how it was, but please note, that I am not paskening halacha lima'aseh, where you could go on Har Habayis and where you can't, and you shouldn't go on Har Habayis at all, as said by most Poskim, that we should not go on Har Habayis.
The first thing we need to do is figure out where the Kodesh HaKodoshim was. We know that the Rambam went onto Har Habayis, so it must be that in the Rambam's times they knew exactly where the Beis Hamikdash was. R' Binyamin from Toledo, who lived the same time as the Rambam, writes (26 אוצר מסעות עמוד) that in Yerushalayim there is a church called Templum Domini, (that is what The Dome of the Rock was called when the crusaders ruled Yerushalayim), which is the place of the Beis Hamikdash, and Omar built a big dome over there. This could prove that The Dome of the Rock is the place of the Beis Hamikdash. Although you could say he means Mizbeach, since until two hundred years ago, almost everybody who dealt with this question, said that The Dome of the Rock is the place of the Kodesh Hakodoshim, that is most probably where it was.
Next, we need to see how big an Amah is. I am using Rabbi Avraham Chayim Na'eh's amah, which is 18.9 inches, or 48 centimeters. Now we need to draw a 9.6 meter square (20 by 20 amos) on the rock for the Kodesh Hakodoshim. There is an argument where exactly in the Kodesh Hakodoshim the rock was, in the east (Tosfos Bava Basra 25a), west (Rambam Beis Habechirah 4:1, and Rashbam bava basra 99a), or center (Rashi megillah 10b). But, we don't have to decide between these different opinions, because the rock is bigger than that, it is 18 by 14 meters. After doing this, I drew the whole Azarah.
The next thing we need to do is draw Har Habayis. I used the Tosfos Yom Tov's (Middos 2:1) numbers of how much space there was between the walls of Har Habayis and the Azarah (250 amos in the south, 213 in the east, 115 in the north and 100 in the south).
Now, we need to figure out what the early part of the east wall (from the south seam to the north seam) are from, if it is not from the walls of the original Har Habayis, but it is from before Hurdus.
The Tavnis Heichal (2:2:15) writes, that around the Har Habayis was a fifty amah migrash, empty space. Drawing the Migrash around the original Har Habayis, it turns out that it ends in the south by the southern seam, and in the north, If you make the outer wall of the migrash turning a drop, it ends up by the northern seam. Looking at the map, I noticed that by the southeast corner the migrash is more than fifty amos from east to west, and by the southwest corner it is less. The reason for this probably is, that they built the huge outer walls of Har Habayis based on the terrain, so they had to make it more than fifty in the east, and less in the west.
I have added sixteen pictures of the third Beis Hamikdash, as well as a new map of it.
My name is Mendel Lewis.
Hashem said to Yechezkel, "Its reading in the Torah is as great as its building. Go and say it to them, and they will occupy themselves to read the form of it in the Torah. And in reward for its reading, that they occupy themselves to read about it, I count it for them as if they were occupied with the building of it. (Tanchuma tzav 14)