In a previous post I brought down the Radvaz's answer (שו"ת הרדב"ז סימן תרל"ט) about why the Har Habayis is now shorter than the rest of Yerushalayim. However, from that teshuva it is not clear by how tall the Radvaz holds the Har Habayis was. From the fact that he brings a proof from the Even Hashesiyah, it seems like he only means that it got a little bit smaller. However, the Radvaz asks this question also in his peirush on the Rambam (Beis Habechirah 6:5), where he asks it about why Har Hazeisim is taller than the Har Habayis, and he gives the same answer, that Har Habayis used to be taller. From this we can see that he holds that Har Habayis used to be much taller, because Har Hazeisim is over 800 meters above sea level, and Har Habayis is now only 740 meters above sea level.
I also want to suggest another reason why Har Habayis is so much shorter. The Zohar (Pekudei, 240b) says that the foundations of the Beis Hamikdash were all hidden, and the enemy did not have power over them. Since the foundations were hidden, it explains why so much of the Har Habayis is "missing". (Although you could ask, some of the foundations are still there, so what is the Zohar saying? I think you could answer this by saying that only the foundations of the square Har Habayis were hidden, and this explains at last fifty amos of the mountains lowering.)
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)