In your second question, I’m not sure what you mean by the difference between Mirashei Aggada and Toras Kohanim. The differences I see are that Medrash is not necessarily written by Tanoim or even Amoraim; it depends on which Medrash. Also, Medrash is not as clear of mistakes as the other Seforim that were constantly learned. Lastly, we don’t Pasken from Aggada.
This last idea has a few parts to it. First of all, as I wrote earlier, we can’t act on what we see as the reason for a Mitzva, since we never can get to the bottom of it with Sevara. We were given the rules and ways to derive the proper Halacha from the Torah. In fact, as the Maharal writes, we go the opposite direction: First we figure out the Halacha, and from there we gain an insight into the reasons for the Mitzva.
Second of all, Aggadeta Gemaros aren’t sifted and ground by Chazal. Therefore, we can’t be sure we really know when and where to apply it.
There is of course the famous reason too, that often times it is not meant to taken literally.
Of course nothing takes away from a clear cut Gemara (usually). However, when something is not discussed in Bavli, we follow Yerushalmi. If it isn’t discussed there either, than we’d follow Medrash, too. The Rambam even Paskens sometimes like a Torahs Kohanim rather than a Gemara. The Or Hachaim explains that the Rambam held that the Amoraim didn’t have the whole Torahs Kohanim, and had they seen it, they too would have agreed.
One more thing. Let’s keep in mind that all Mitzvos have a reason in Sohd. Even when Reb Shimon argues with another Tanna in the Mishna, we don’t say that since Reb Shimon knew the ‘real’ meaning, we should listen to him. As mentioned above, the Halacha is known from the regular ways, the 13 methods. Reb Shimon Bar Yochai, who excelled in Sohd, was able to know the hidden meaning behind the Halacha. That means that ‘after class’ he would tell his students the hidden reason for the Halacha as he Paskened and the hidden reason for the Halacha as his friend Paskened.
Now we can get back to the issue at hand. If the Zohar Hakadosh differs from the Gemara, we obviously Pasken like the Gemara. The thing gets sticky when we have Rishonim that already Paskened a certain way and then the Zohar Hakadosh was found. The Metzaref Lechachma, by the Yashar MiCandia (or Canadia) – Reb Yosef Shalom Rofei (lived around 1550) – writes that when the Halacha is already established, we must follow the established Halacha. Otherwise, we listen to the Zohar Hakadosh. When the Zohar Hakadosh says directly to do or not to do something, that for us is not following Sevara. As to how Reb Shimon Bar Yochai was able to say what to do based on Sohd, it says about him, Bechal Besi Ne’eman Hu.
By today, it sort of breaks down to how Sohd oriented you are. Some people ignore any Zohar Hakadosh until some Posek will quote it. Others follow it with a similar approach as the Metzaref Lechachma. Those who relate more to Sohd will follow Sohd as much as possible. This is where the Teffilin on Chol Hamoed comes in. If not for the Zohar Hakadosh, the usual rules of Paskening would have everyone donning Teffilin on Chol Hamoed.
One more thing: Following Sohd is not totally like acting on an Aggadaic, philosophical, Drush, Psychological, sweet or simple reason. Sohd is an understanding of the ‘real’ reason. However, we still always keep in mind that the Mitzvos are much deeper than our understanding. Although all Torah Lishma is real of course, the other explanations are like offshoots of the main trunk, while the Sohd is the trunk. Therefore, those with a true understanding of the Sohd, can be Machria the Halacha toward the Sohd.