In several classes of countable structures it is known that every hyperarithmetic structure has a computable presentation up to bi-embeddability. In this article we investigate the complexity of embeddings between bi-embeddable structures in two such classes, the classes of linear orders and Boolean algebras. We show that if $mathcal L$ is a computable linear order of Hausdorff rank $n$, then for every bi-embeddable copy of it there is an embedding computable in $2n-1$ jumps from the atomic diagrams. We furthermore show that this is the best one can do: Let $mathcal L$ be a computable linear order of Hausdorff rank $ngeq 1$, then $mathbf 0^{(2n-2)}$ does not compute embeddings between it and all its computable bi-embeddable copies. We obtain that for Boolean algebras which are not superatomic, there is no hyperarithmetic degree computing embeddings between all its computable bi-embeddable copies. On the other hand, if a computable Boolean algebra is superatomic, then there is a least computable ordinal $alpha$ such that $mathbf 0^{(alpha)}$ computes embeddings between all its computable bi-embeddable copies. The main technique used in this proof is a new variation of Ash and Knights pairs of structures theorem.
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