Let $F_n$ denote the free group on $n$ generators and let $S_k$ denote the symmetric group on the integers $\{1,\dots, k\}$, and the action of homomorphism $\phi$ (as given in the title) on the generators of $F_n$ be known. Let $K_{\phi}$ denote the kernel.
My question is two-fold.
I've had GAP spit out a couple dozen random examples of such homomorphisms/kernels and in every case so far $K_{\phi}$ appears to be of infinite generation. Is this always the case? I can't imagine how it couldn't be if $\phi$ is chosen to be nontrivial (my reasoning is that, even if $\phi$ kills off all but one generator, so that $K_{\phi}$ is a subset of an infinite cyclic subgroup of $F_n$, $K_{\phi}$ is still not finitely generated, and if $\phi$ kills off fewer-than-all-but-one generators the complexity only increases) but I also can't see how I would begin a proof, unless my reasoning in the previous parenthetical is the proof strategy. (Supposing, though, that there is a counterexample, is there a way to tell from the presentation of $\phi$ whether or not $K_{\phi}$ is finitely-presented?)
Can anything be said about the "combinatorics" of the embedding $\iota: K_{\phi} \hookrightarrow F_n$? (To clarify what I mean by this: Of course, if all the groups that arise as kernels in this way are on infinite generators then any two are isomorphic by Nielsen-Schrier, but even if two such arise from the same $F_n$, they're clearly not necessarily the same subgroup.)
Edit: I seem to have forgotten or never learned something important--As James points out in a comment below, $K_{\phi}$ is a finite-index subgroup of a finitely-generated group, so it's necessarily finitely-generated by what I just learned is called Schreier's lemma. With that in mind, I think it's sensible to revise the first part of my question to "What can we say about a generating set of $K_{\phi}$ given what we know about $\phi$?" The second part of the question remains a question for the time being.
I've given this the reference request tag in case there's a standard source on these topics that I should be familiar with. If anything is unclear, please post a comment and I'll try to fix it.