This paper is a continuation of the author's previous work, where we studied one of the inequalities between the characteristic ideal of the Selmer group and the ideal of the $p$-adic $L$-function predicted by the two-variable Iwasawa main conjecture for a nearly ordinary Hida deformation $\mathcal{T}$. In this paper, we study several properties of the Selmer group and the $p$-adic $L$-function solving some of the open questions raised in the author's previous work. As applications, we have an infinite family of elliptic cuspforms where the cyclotomic Iwasawa main conjecture holds for every cuspform in the family.