heretofore –
We do pasken from the gemara. When what seems to be in the gemara seems to go against a halacha in Shulchan Aruch we will normally follow the halacha in S.A. because R’ Yosef Karo probably knew the gemara better than you and me, but regarding something that isn’t written in the S.A. we definitely pasken from the gemara. Most sheilos u’tshuvos seforim do that.
R’ Moshe’s sons R’ Dovid and R’ Reuven are widely regarded as great gedolim and poskim. Someone told a relative of mine that he asked R’ Elyashiv a serious halacha sheila that had to do with someone in America, and R’ Elyashiv asked if the guy had already asked R’ Dovid Feinstein. When the guy told him no, R’ Elyashiv told him to go ask R’ Dovid. From what I know, all the major poskim nowadays hold of him very strongly.
When he told the person ‘it’s not your business’ it was because being a ba’al nefesh is a personal thing and has to come from a deep understanding of oneself. He most probably held that no benefit would come to this person from knowing this piece of personal information, though as I said, he only said that half-seriously. I don’t think he needs to be excused for not wanting to discuss his private relationship with Hashem with any random person. As for the halacha that we need to know, he is clear about his position that there is no problem whatsoever with c.s.
I understand that you are just trying to learn, and I commend your efforts, and I’m doing my best to inform you what I know.