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Your question is entirely covered by Section 2 of Brain–Mesland–Van Suijlekom, but the fgp case is simple enough to ultimately boil down to folklore proved by Chakraborty–Mathai. Let me summarise what happens, while incorporating some technical simplifications from Blecher–Kaad–Mesland. For convenience, let $\Omega_D$ be the unital $C^\ast$-subalgebra of $B(H)$ generated by $A$ and $[D,\mathcal{A}]$.

1. Let $\mathcal{A} := \{a \in A \mid a \operatorname{Dom}(D) \subset \operatorname{Dom}(D),\, [D,a] \in B(H)\}$ be given the Lipschitz norm $\|a\| := \|a\| + \|[D,a]\|$. Then $\mathcal{A}$ defines an involutive operator algebra and the inclusion $\mathcal{A} \hookrightarrow A$ is completely bounded with dense range that is closed under the holomorphic functional calculus; in particular, it follows that $M_N(\mathcal{A})$ is dense in $M_N(A)$ and closed under the holomorphic functional calculus for any $N \in \mathbb{N}$. You should think of $\mathcal{A}$ as defining a Lipschitz structure on the NC space $A$.
2. Let $\mathcal{E}$ be a dense subspace of $E$ satisfying $\mathcal{E} \cdot \mathcal{A} \subset \mathcal{E}$ and $(\mathcal{E},\mathcal{E})_A \subset \mathcal{A}$. By part 1 and the properties of $\mathcal{E}$, we can find $A$-module generators $\{\xi_1,\dotsc,\xi_N\} \subset \mathcal{E}$ for $E$, such that $$ \forall e \in E, \quad e = \sum_{i=1}^N \xi_i \cdot (\xi_i,e)_A. $$ Thus, if $p := \left((\xi_i,\xi_j)_A\right)_{i,j=1}^N \in M_N(\mathcal{A})$, then $e \mapsto \left((\xi_i,e)_A\right)_{i=1}^N$ defines an isomorphism $E \cong pA^N$ of Hilbert $A$-modules that restricts to an isomorphism $\mathcal{E} \cong p\mathcal{A}^N$ of pre-Hilbert $\mathcal{A}$-modules; this now makes $\mathcal{E}$ into a (finitely generated) projective operator module over $\mathcal{A}$ in a manner that depends on the choice of $\{\xi_1,\dotsc,\xi_N\}$ only up to completely bounded isomorphism. You should think of $\mathcal{E}$ as defining a Lipschitz structure on the NC vector bundle $E$; since $E$ is fgp, this Lipschitz structure is canonically induced by the choice of Lipschitz structure on $A$.
3. Let $\mathcal{B} := \{b \in B \mid b \cdot \mathcal{E} \subset \mathcal{E}\}.$ Since $$ \mathcal{B} = \left\{b \in B \mid \left((\xi_i,T\xi_j)_A\right)_{i,j=1}^N \in M_N(\mathcal{A})\right\}, $$ it follows that $\mathcal{B}$ is $\ast$-closed and that the $\ast$-isomorphism $B \cong p M_N(A) p$ induced by the Hilbert $A$-module isomorphism $E \cong p A^N$ restricts to a $\ast$-isomorphism $\mathcal{B} \cong p M_N(\mathcal{A}) p$. Thus, $\mathcal{B}$ can be topologised as a closed $\ast$-subalgebra of the involutive operator algebra $M_N(\mathcal{A})$, thereby making $\mathcal{E}$ into a Lipschitz $(\mathcal{B},\mathcal{A})$-correspondence. In particular, you can view $\mathcal{B}$ as defining a Lipschitz structure on the NC space $B$ compatible with the Lipschitz structure $\mathcal{A}$ on the NC space $A$.
4. Let $\nabla : \mathcal{E} \to E \hat\otimes_A \Omega_D$ be a Hermitian connection, i.e., a completely bounded $\mathbb{C}$-linear map satisfying $$ \forall e \in \mathcal{E},\, \forall a \in \mathcal{A}, \quad \nabla(ea) = \nabla(e)a + e \hat\otimes [D,a],\\ \forall e_1,e_2 \in \mathcal{E}, \quad (\nabla(e_1),e_2 \hat\otimes 1)_{\Omega_D} +(e_1 \hat\otimes 1,\nabla(e_2))_{\Omega_D} = [D,(e_1,e_2)_A]; $$ for example, the Graßmann connection $\nabla_0$ induced by the frame $\{\xi_1,\dotsc,\xi_N\}$ is defined by $$ \forall e \in \mathcal{E}, \quad \nabla_0(e) := \sum_{i=1}^N \xi_i \hat\otimes [D,(\xi_i,e)_A], $$ and indeed, if $\nabla$ is any other Hermitian connection, then $\nabla = \nabla_0 + \omega(\cdot \hat\otimes 1)$ for $\omega \in \operatorname{End}_{\Omega_D}(E \hat\otimes_A \Omega_D)$ defined by $$ \forall e \in \mathcal{E}, \, \forall \eta \in \Omega_D, \quad \omega(e \hat\otimes \eta) := \sum_{i=1}^N \nabla(\xi_i)(\xi_i,e)_A\eta. $$ Then, by