> But I am completely lost at how to reason about the limits of integration here.
Yes, and this is because the densities are **not** what you write. Rather, $f_X$ and $f(\ \mid x)$ are defined on the whole real line $\mathbb R$ by $$ f_X(x)=\mathbf 1_{0\lt x\lt 1},\qquad f(y\mid x)=\frac1x\cdot\mathbf 1_{0\lt y\lt x}. $$ Note that $f_X(x)$ exists for every $x$ and that, if $x$ is in $(0,1)$, $f(y\mid x)$ exists for every $y$. One usually extends $f(\ \mid x)$ by $f(y\mid x)=0$ for every $y$ if $x$ is not in $(0,1)$. Then, as you explained, for every $y$, $$ f_Y(y)=\int_{-\infty}^{\infty}f_Y(y\mid x)f_X(x)\mathrm dx, $$ that is, $$ f_Y(y)=\int_0^1\frac1x\mathbf 1_{0\lt y\lt x}\mathrm dx=\mathbf 1_{0\lt y\lt 1}\int_y^1\frac1x\mathrm dx=\text{____}\cdot\mathbf 1_{0\lt y\lt 1}. $$