For the intermediate question (a core with three top-bottom runs), how about this?

Some notation: I will be describing runs by words in $\{l,r\}^*$, with e.g. $llrl$ corresponding to a subgraph $\cdot\leftarrow\cdot\leftarrow\cdot\to\cdot\leftarrow\cdot$. The level increases on $r$ arcs and decreases on $l$ arcs, and I assume that its minimum is $0$. Some straightforward constraints are:

 - There cannot be a run consisting only of $l$s or only of $r$s, because otherwise there is an obvious homomorphism from $D$ to this run (mapping each node of $D$ to the one with the same level). This also implies that the maximum level must be at least $3$.
 - If the maximum level were $3$, then all top-bottom (resp bottom-top) runs would be of the form $llr(lr)^ill$ (resp. $rrl(rl)^irr)$; again it is not very hard to find a homomorphism from $D$ to the run which minimizes $i$. 

However, for maximum level $4$ there is a solution, of length $36$: consider $D$ given by $(rrrlrrlllrll)^3$. Unless I missed something, this is a core, and by the above constraints, it is necessarily minimal, since each run only has a single "backwards" edge.