[guided]The delicate point is that the moving frame contributes four Ricci-linear terms, and those terms must cancel with the linear part of the covariant curvature evolution before the curvature can be regarded as satisfying a clean heat-type equation on the fixed bundle $\Lambda^2E$.
We use the curvature sign convention
\begin{align*}
R_{g(t)}(X,Y,Z,W)=g(t)((\nabla^{g(t)}_X\nabla^{g(t)}_Y-\nabla^{g(t)}_Y\nabla^{g(t)}_X-\nabla^{g(t)}_{[X,Y]})Z,W)
\end{align*}
for smooth vector fields $X,Y,Z,W\in\mathfrak X(U)$. Since $g(t)$ is a smooth Ricci flow on $U\times J$, all curvature tensors and covariant derivatives in the following identity are smooth. These are exactly the regularity hypotheses required for Hamilton's covariant curvature evolution identity for a smooth Ricci flow, the standard covariant tensor evolution formula from Hamilton's Ricci-flow curvature computation. In this sign convention, the identity says that
\begin{align*}
(\partial_t R_{g(t)})(A,B,C,D)=(\Delta_{g(t)}R_{g(t)})(A,B,C,D)+Q_{g(t)}(A,B,C,D)-R_{g(t)}(\operatorname{Ric}_{g(t)}^{\sharp}A,B,C,D)-R_{g(t)}(A,\operatorname{Ric}_{g(t)}^{\sharp}B,C,D)-R_{g(t)}(A,B,\operatorname{Ric}_{g(t)}^{\sharp}C,D)-R_{g(t)}(A,B,C,\operatorname{Ric}_{g(t)}^{\sharp}D),
\end{align*}
where, in a local $g(t)$-orthonormal frame $(e_1,\dots,e_n)$, the tensor $Q_{g(t)}$ is defined by
\begin{align*}
B_{i j k l}=\sum_{p,q=1}^n R_{p i q j}R_{p k q l},\qquad
Q_{i j k l}=2(B_{i j k l}-B_{i j l k}-B_{i l j k}+B_{i k j l}).
\end{align*}
The displayed factor $2$ is a normalization statement, not a cosmetic convention: with the curvature operator defined by
\begin{align*}
h_{\Lambda^2}(\mathcal R(u\wedge v),w\wedge z)=R_{g(t)}(\iota_tu,\iota_tv,\iota_tw,\iota_tz),
\end{align*}
this tensor $Q_{g(t)}$ corresponds to $2(\mathcal R^2+\mathcal R^{\#})$.
Now substitute Hamilton's identity into the time derivative formula from the previous step. The four terms produced by differentiating the moving frame are
\begin{align*}
R_{g(t)}(\operatorname{Ric}_{g(t)}^{\sharp}A,B,C,D)+R_{g(t)}(A,\operatorname{Ric}_{g(t)}^{\sharp}B,C,D)+R_{g(t)}(A,B,\operatorname{Ric}_{g(t)}^{\sharp}C,D)+R_{g(t)}(A,B,C,\operatorname{Ric}_{g(t)}^{\sharp}D).
\end{align*}
These are exactly the negatives of the four Ricci-linear terms in Hamilton's covariant evolution identity, so they cancel term by term. Therefore
\begin{align*}
\partial_t \mathcal R_{a b c d}=(\Delta_{g(t)}R_{g(t)})(A,B,C,D)+Q_{g(t)}(A,B,C,D).
\end{align*}
Finally, $\iota_t$ intertwines the pulled-back connection $\nabla^E(t)$ with $\nabla^{g(t)}$, and the trace defining the rough Laplacian is taken over corresponding orthonormal frames. Hence
\begin{align*}
(\Delta_{g(t)}R_{g(t)})(A,B,C,D)
=
h_{\Lambda^2}\bigl((\Delta_{\nabla^E(t)}\mathcal R)(a\wedge b),c\wedge d\bigr).
\end{align*}
This gives the pulled-back evolution
\begin{align*}
\partial_t\mathcal R=\Delta_{\nabla^E(t)}\mathcal R+\mathcal Q(\mathcal R),
\end{align*}
where $\mathcal Q(\mathcal R)$ is the endomorphism of $\Lambda^2E$ determined by the pulled-back tensor $Q_{g(t)}$ through $h_{\Lambda^2}$.[/guided]