Rabbeinu Tam (in Tosfos 83a DH uk'Divrei) says that on Erev Yom Kipur, people only slaughtered birds - not large animals.
Granted, he cites a source from a Midrash. But why does he overlook 95b, which says that on Erev Yom Kipur, ravens dropped livers and kidneys and Rav Nachman permitted them because most meat slaughtered that day is Kosher. Surely, this does not only refer to organs of fowl!
Also, we find on 110a that Rami bar Tamri came to Sura on Erev Yom Kipur and saw everyone discarding udders. He gathered them and ate them. Can't we assume that the cows were slaughtered that day? If everyone slaughtered the day before, since they forbid udder in Sura they should have discarded them immediately!
Perhaps Rabeinu Tam holds that the custom changed from the days of the Tana'im to the days of the Amora'im. But then he should have said so!
Pesach Feldman
1. The Rashash (95b) writes that apparently the Gemara there follows Rebbi Yosi ha'Glili in the Mishnah (83a) who disagrees with the Tana Kama there and maintains that on Erev Yom Kippur, one also slaughters large animals. He also implies that the Gemara (110a) which you have cited also is consistent with the view of Rebbi Yosi.
2. You write that since they forbid udder in Sura, they should have discarded them immediately. I would like to argue that it would not be necessary to do so, and it would be permitted for them to keep them, since they might find Nochrim interested in buying them. The Gemara earlier (53b) suggests that it may be only if one leaves a prohibited item around for 12 months that there is a concern that one will come to eat it. Rashi there (DH li'Yedei) writes that since a lot of Safek Tereifos were kept, one cannot be careful with them and will come to eat one of them. However, if one keeps an item of Safek Isur for only 21 days, there is no concern that during this short period of time he will come to eat it. The proof for this is from the Gemara in Chulin (58a) concerning the eggs of a bird which is a Safek Tereifah. If one keeps the mother until she bears a new set of eggs, this proves that she is not a Tereifah, and therefore the first set of eggs are also permitted. The Shulchan Aruch (YD 86:9) says that this is a period of 21 days. The Taz (#16) writes that 12 months is a long time, and one is concerned about "Takalah" during this period, while for the short period of 21 days one is not afraid that a mistake will occur.
3. I would also like to suggest a different solution for the apparent contradictions concerning whether one should eat poultry or animal meat on Erev Yom Kippur. It seems to me that this is a question of custom with no particular Halachic mandate involved here. In most, but not all, places in Eretz Yisrael we see from the Mishnah (83a) that they ate poutlry. However, the Gemara (95b and 110a) refers to the practice in Bavel. Possibly animal meat was more prevalent in Bavel than poultry. If this is correct, this would also explain the Gemara (133a) where Abaye says that it was only on Erev Yom Kippur that he was prepared to receive the presents to which he was entitled as a Kohen. Tosfos (DH l'Bar) explains that many presents were given to the Kohanim on Erev Yom Kippur. The presents given to the Kohen are from animals, not birds. It is possible that since Abaye was in Bavel, the custom was to eat animal meat there on Erev Yom Kippur. You write that if Rabeinu Tam maintained that the custom changed between the times of the Tana'im and the Amora'im, he should have said so. However, it seems to me that it may not have been necessary for him to say so because on 83a he is merely commenting on the Mishnah.
Kol Tuv,
Dovid Bloom
I asked a Gadol how Rabeinu Tam learns the Gemara on 110a that everyone threw out their udders on Erev Yom Kippur and ate the rest of the meat. Birds do not possess udders!
He answered that apparently in Sura they had no choice but to eat animal meat. Possibly in Bavel poultry was not easily available, and therefore even according to Rabeinu Tam animal meat was eaten on Erev Yom Kippur.
Dovid Bloom