WAS THE ARON HIDDEN OR EXILED?
The Mishnah implies that the Aron was exiled.
There are two opinions (R. Eliezer and R. Shimon b. Yochai) which maintain that it was exiled (based on two different Pesukim) and one which maintains that it was hidden in its place, and remains so, based on the words "Ad ha'Yom ha'Zeh".
According to Ula, R. Shimon b. Yochai is of the opinion that the Aron is hidden.
Ula reported an exchange between R. Masia b. Charash and R. Shimon b. Yochai.
Question: Are all occurrences of "Ad ha'Yom ha'Zeh" meant to be taken literally?
The Pasuk speaks of the Yevusi living in Yerushalyaim "Ad ha'Yom ha'Zeh".
We know from Yirmeyahu that there were 52 years of total desolation (like the numerical value of 'Beheimah').
We also know (from R. Yosi in the Beraisa) that Gafris and Melach alone reigned in Eretz Yisrael for seven years (compare "B'ris"-"B'ris").
Answer: The word "Sham" adds the real impression of forever.
Question: But we find an instance of "va'Yeishev Sham" which was interrupted by Sancheriv?
Answer: Good question.
WHERE WAS THE ARON HIDDEN?
Chachamim (cited by R. Nachman) taught that the Aron is beneath the wood-checking Lishkah.
A tragic incident reported in the Beraisa supports the claim that the Aron is not beneath the Kodesh ha'Kodoshim.
In the incident a Kohen, engaged in another activity, died while trying to point out the place of the Aron to the other Kohanim.
Question: What was that Kohen doing?
Answer: He was using his ax (as confirmed by the tragic incident reported by a Tana d'bei R. Yishmael).
THE VISIBLE/INVISIBLE BADIM
Question: The (cited) Pesukim seem to contradict one another?!
Answer: The Badim were both visible and invisible.
Further, they miraculously extended in order to be visible from without.
The refrained from extending too far (which would tear the Paroches) and only pushed out slightly, like a woman's breasts through her garment.
THE INTIMATE BOND BETWEEN THE PEOPLE AND HASH-M
(R. Katina): The bond was revealed to the people by opening the Paroches during Aliyas Regel (the embracing Keruvim).
Question: But the Pasuk teaches that the Keilim of the Mishkan may not be seen!?
Answer: The Mishkan was likened to a Kalah before her wedding while the Beis ha'Mikdash was like a Kalah after her wedding.
Question: But we find that a Kohen was killed in order to prevent the possible exposure of the Aron!?
Answer: That was during the second Mikdash, when the remarried wife is, again, like the Kalah before the Chupah.
Question: Then R. Katina's teaching cannot apply to either Mikdash!?
The first Beis ha'Mikdash did not have a Paroches.
The second Beis ha'Mikdash did not have Keruvim.
Answer: He spoke of the first Beis ha'Mikdash and the Paroches refer to the (many door) coverings (as enumerated).
Alternate Answer: He spoke of the second Beis ha'Mikdash and they showed the people the Keruvim as part of the wall decorations.
Those Keruvim were very noticeable as supported by two Pesukim.
The second of those Pesukim refers to the Keruvim as being made "ke'Ma'ar Ish ve'Loyos".
What is "ke'Ma'ar Ish ve'Loyos"?
Like a man embracing his wife.
The destroyers of the Mikdash mocked the intimate Keruvim (thus fulfilling the prophecy of "Kol Mechabdehah Hiziluhah").
THE EVEN HASHESIYAH
It was called 'Shesiyah' because the world was founded on it.
This is consistent with view of Chachamim that the world was created from Tzion.
This is a four-way Machlokes in the Beraisa.
R. Eliezer (it was created from its center), R. Yehoshua (it was created from its sides), R. Yitzhok (from the stone which Hash-m fired into the sea), and the Chachamim (from Tzion).
R. Eliezer ha'Gadol taught that the Shamayim was created from Shamayim and the Aretz from Aretz, while the Chachamim say that they were both created from Tzion.