(a) On daf 54B, we establish that there are occasions where there would be more than 48 t'kios, but the mishna is only listing those that on a yearly basis.
If true then how did we answer the gemorah earlier question on R" ACHA of MAY SHAYAR DHAI SHAYAR? The two examples of Rosh Hashanah on Shabbos and Pesach on Erev Shabbos would never have been included in the mishna for they are not yearly occupancies?
(b) In your insites to 55:3 you bring an answer from the Aruch Laner as to why the Korban Ha'omer was not brought as an example of something which is divided to all Kohanim, due to the fact that it is not primarily to be brought on the first day of Yom Tov. Doesn't the PAREI HACHAG demonstrate that even korbanos which are not to be brought on the first day still divided amongst all Kohanim?
(a) You are correct -- once the Gemara establishes that the Mishnah is only referring to occasions which occur on a yearly basis, there is no longer a need to explain what the Mishnah left out; it did not leave out anything, as you wrote, and there is no question on Rav Acha, because the Mishnah is not discussing occasions that do not happen yearly.
When the Gemara mentions Rosh Hashanah that falls on Shabbos, it is not attempting to answer "Mai Shayar d'Hai Shayar," rather it is asking on Rav Acha that this is the only occasion left out of the Mishnah. As you wrote, this occassion is no longer left out, and therefore no further answer need be given for Rav Acha.
(b) Good question. The ARUCH LA'NER deals with your question, and writes that the Korbanos Musafim of each day are different than the Korban ha'Omer, because "all the Musafim are compared to one another." (In Sukah 55a the Gemara compares "all the Roshei Chadoshim to each other," and in Shavuos 10a it compares all the Se'irim of the Moadim to each other.)
Best wishes, and my apologies for the delay,
M. Kornfeld