Hi @MVEverett ,
I have not tried this, nor am I working with 18S data. Just want to comment briefly in case it provides some leads.
First, I had a quick look at taxmap_ncbi_ssu_ref_nr99_138. Although it has Onchorhynchus mykiss and Onchorhynchus kisutch, I am not seeing any Onchorhynchus tshawytscha. So swapping the taxmaps as you propose might technically work, but you will still be missing what I assume is a key taxonomic lineage for you, though maybe that's okay if you just want to get to genus level. (I have not tried swapping these)
You might also check out the action get-ncbi-data to create a custom NCBI 18S classifier instead. Or RESCRIPt has actions for some 18S-specific databases like eukaryome and PR2, these could be worth a shot if you want to compare some different options.
Good luck!