[guided]The only term left to compute is the part caused by replacing $\Delta$ with $L$. Define
\begin{align*}
D_f:M\to\mathbb R
\end{align*}
by
\begin{align*}
D_f=-\frac{1}{2}g(\nabla V,\nabla|\nabla f|^2)+g(\nabla f,\nabla g(\nabla V,\nabla f)).
\end{align*}
We want to show that this equals $\nabla^2V(\nabla f,\nabla f)$. Fix a point $p\in M$. Set $X=\nabla f$ and $Y=\nabla V$ as smooth vector fields on a neighbourhood of $p$.
First compute the derivative of the squared norm of $X$ in the direction $Y$. The Levi-Civita connection is metric-compatible, so for the function $|X|^2=g(X,X)$,
\begin{align*}
Y(|X|^2)=2g(\nabla_YX,X).
\end{align*}
Thus
\begin{align*}
\frac{1}{2}g(\nabla V,\nabla|\nabla f|^2)=\frac{1}{2}Y(|X|^2)=g(\nabla_YX,X).
\end{align*}
Next compute the derivative of the function $g(Y,X)$ in the direction $X$. Again using metric compatibility and the product rule,
\begin{align*}
X(g(Y,X))=g(\nabla_XY,X)+g(Y,\nabla_XX).
\end{align*}
In the original notation this is exactly
\begin{align*}
g(\nabla f,\nabla g(\nabla V,\nabla f))=g(\nabla_XY,X)+g(Y,\nabla_XX).
\end{align*}
Now compare the two terms involving the Hessian of $f$. Since $X=\nabla f$, the covariant derivative of $X$ is the Hessian of $f$: for vector fields $A$ and $B$,
\begin{align*}
g(\nabla_AX,B)=\nabla^2f(A,B).
\end{align*}
The Hessian of a smooth real-valued function is symmetric because the Levi-Civita connection is torsion-free. Therefore
\begin{align*}
g(\nabla_YX,X)=\nabla^2f(Y,X)=\nabla^2f(X,Y)=g(\nabla_XX,Y).
\end{align*}
By symmetry of the metric, $g(\nabla_XX,Y)=g(Y,\nabla_XX)$. Hence the two $f$-Hessian terms cancel:
\begin{align*}
D_f=-g(\nabla_YX,X)+g(\nabla_XY,X)+g(Y,\nabla_XX)=g(\nabla_XY,X).
\end{align*}
Finally, because $Y=\nabla V$, the Hessian of $V$ satisfies
\begin{align*}
\nabla^2V(X,X)=g(\nabla_X\nabla V,X)=g(\nabla_XY,X).
\end{align*}
Substituting $X=\nabla f$ gives
\begin{align*}
D_f=\nabla^2V(\nabla f,\nabla f).
\end{align*}[/guided]