In the light of the Hadith from one of the imams (as) that goes something like “He is not from our Shias who does not read atleast 50 verses of the Quran per day”. I wanted to know if this talks about 50 separate apart from the regular surahs that are recited each day eg sure Yasin, sure Waqia, etc. Ofcourse, the aim should be reading maximum Quran ayats but I just wanted to have this clarified.

It is about reading 50 verses, as you want.
It is not necessary to be from one surah.