The Shulchan Aruch (147:8) rules that on a day where we read from two sifrei Torah, one is not allowed to open the second until the first covered. The Rama adds that the first sefer Torah is not removed until the second one has been placed on the bima. He explains that this is to ensure there is no break between one mitzvah and the next. Why are we discussing this halacha? How does it relate to the Mishnayot we learnt this week? We will see that the source of this halacha is found in the Mishnah.
The Magen Avraham explains that this law is found in the Or Zarua that cites our Mishnah as the source. During the week, we learnt how the blood from the bull and goat were sprinkled in the kodesh ha'kodashim, in front of the parochet and on the mizbeach ha'zahav. The Mishnah records a debate how, when the kohen exited from the kodesh ha'kodashim with the blood from the goat, he would exchange it for the blood from the bull. R' Yehuda explains that there was only one stand to hold the blood. Consequently, he would take the bull's blood off first (with his right hand) and then put down the goat's blood. The Chachamim however explains that there were two stands. Consequently, the goat's blood was put down first, then the bull's blood was taken.
The Or Zarua derives our law from the opinion of R' Yehuda. Since the object (the blood) of the second mitzvah was taken prior to returning the first, we place the second sefer Torah on the bima prior to wrapping up the first.
The Magen Avraham however asks that the opinion of the Chachamim appears to contradict this law. Recall that the goat's blood was placed on the stand first, prior to taking the bull's blood! The Magen Avraham however suggests that perhaps that case is different. If, according to the Chachamim, the kohen gadol would take the bull's blood first, he would being doing so with his left hand. The blood however needs to be collected with his right hand. Consequently, it is preferable in this case to put the goat's blood down first thereby enabling the kohen gadol to use his right hand to take the bull's blood.
The Minchat Yitzchak (II 117:1) however is surprised why the Magen Avraham did not ask a stronger question. Granted that the proof is brought from the opinion of R' Yehuda, since according to his opinion there was only one stand, the kohen gadol had no other option but to take the bull's blood first. Consequently, it is a weak proof for our law.
Perhaps we can this question based on a comment of the Tosfot Yom Tov. The Gemara asked why according to R' Yehuda there was only one stand. The Gemara initially answers that if there were two stands, R' Yehuda was concerned that the two containers would get mixed up. The Gemara initially assumes that the even if the stands were labelled, R' Yehuda would still be concerned that the kohen gadol would not be conscious of the labels and still end up with the bloods be switched in error. The Gemara ultimately rejects that suggestions, since we find that R' Yehuda was satisfied with the labels on the shofarot (money chests) in the Beit HaMikdash. So why then was there only one stand? The Tosfot Yom Tov suggests that according to R' Yehuda there was simply no need for a second stand. He could simply remove the bull's blood prior to placing the goat's blood on the stand.
Based on the Tosfot Yom Tov, perhaps the proof is not just from the order suggested by R' Yehuda. But rather if the order should have been reversed, then R' Yehuda would have used a second stand. The fact that a single stand was sufficient, demonstrates a preference for the next mitzvah to be taken prior to returning the first.
The continuation of the Gemara also seems to suggest that the order according to R' Yehuda is deliberate. The Gemara cites an incident where Rava corrected a shaliach tzibur that described two stands, yet the bull's blood being taken prior to the goat's blood. Rava commented that you are doing one (two stands) like the Chachamim and one (the order) like R' Yehuda.
Admittedly, the Tosfot Yom Tov however continues that the Gemara, just prior to the incident with Rava, concludes that on Yom Kippur, due to the fatigue of the kohen gadol, there was even a greater reason why we would be concerned for a mix-up despite labelling. It is for that reason then the R' Yehuda only allowed one stand. If that is the sole reason, the question of the Minchat Yitzchak still stands.
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