You basically have everything. We just need to extend $(3)$ to all of $\mathcal{D}(A^{\alpha}) \times \mathcal{D}(A^{-\alpha})$.
We endow $\mathcal{D}(A^{\alpha})$ with the inner product $\langle\,\cdot\,,\,\cdot\,\rangle_{\alpha}$ and obtain a Hilbert space that is in an obvious way isometrically isomorphic to the weighted sequence space
$$\ell^2((\lambda_n^{2\alpha}),\mathbb{N}) = \Biggl\{ x \in \mathbb{R}^{\mathbb{N}} : \sum_{n\in\mathbb{N}} \lambda_n^{2\alpha}\lvert x_n\rvert^2 < +\infty\Biggr\}.$$
We can also consider the weighted sequence space
$$\ell^2((\lambda_n^{-2\alpha}),\mathbb{N}) = \Biggl\{ y \in \mathbb{R}^{\mathbb{N}} : \sum_{n\in\mathbb{N}} \lambda_n^{-2\alpha}\lvert y_n\rvert^2 < +\infty\Biggr\}.$$
We have a natural bilinear pairing
$$\langle\,\cdot\,,\,\cdot\,\rangle_{\alpha,-\alpha} \colon \ell^2((\lambda_n^{2\alpha}),\mathbb{N}) \times \ell^2((\lambda_n^{-2\alpha}),\mathbb{N}) \to \mathbb{R};\quad \langle x,y\rangle_{\alpha,-\alpha} = \sum_{n\in \mathbb{N}} x_n y_n.$$
One verifies easily that this bilinear pairing gives isometric isomorphisms $$\ell^2((\lambda_n^{-2\alpha}),\mathbb{N}) \to \ell^2((\lambda_n^{2\alpha}),\mathbb{N})'$$ and $$\ell^2((\lambda_n^{2\alpha}),\mathbb{N}) \to \ell^2((\lambda_n^{-2\alpha}),\mathbb{N})'.$$
On the other hand, we can identify $\mathcal{D}(A^{-\alpha})$ with $\ell^2((\lambda_n^{-2\alpha}),\mathbb{N})$, since we can write
$$\mathcal{D}(A^{-\alpha}) = \Biggl\{ \sum_{n\in\mathbb{N}} y_n e_n : y \in \ell^2((\lambda_n^{-2\alpha}),\mathbb{N})\Biggr\}.$$
Note: the sum is formed in $\mathcal{D}(A^{-\alpha})$, where $\lVert e_n\rVert = \lambda_n^{-\alpha}$, not in $H$, where $\lVert e_n\rVert_H = 1$.
The situation is analogous to the case of Sobolev spaces. We have $H^{-s} = (H^s)'$ by definition for $s > 0$, and the chain of inclusions (where each inclusion is not only strict as an inclusion of sets, also the topology on each space is strictly finer than the subspace topology induced by a larger space in the chain)
$$H^t \subsetneq H^s \subsetneq H^0 = L^2 \subsetneq H^{-s} \subsetneq H^{-t}$$
for $0 < s < t$, but as Hilbert spaces, all the $H^r$ are of course also isometrically isomorphic to their duals. Here, we have for $0 < \alpha < \beta$ the chain of inclusions
$$\mathcal{D}(A^{\beta}) \subset \mathcal{D}(A^{\alpha}) \subset \mathcal{D}(A^0) = H \subset \mathcal{D}(A^{-\alpha}) \subset \mathcal{D}(A^{-\beta}),$$
and if $\lambda_n \to +\infty$, all inclusions are strict and the topology on each space is strictly finer than the subspace topology induced by a larger space in the chain. And like for the Sobolev spaces, we have $\mathcal{D}(A^{-\alpha}) \cong \mathcal{D}(A^{\alpha})'$ by one natural bilinear pairing, and $\mathcal{D}(A^{\alpha}) \cong \mathcal{D}(A^{\alpha})'$ by the Riesz map.