Hi @devonorourke,
Sorry for the delayed response. Thanks for sharing the details of your awesome sleuthing process!
About the primers not always landing where they should… this is the key problem I highlighted here, when it comes to using alignment positions for extraction, see the first bullet.
It might be best to make a very small alignment, in which you know the primers will align properly, then start your process of mapping all your other data to this alignment. I’ve done this before and sometimes with a little manual curation of the primer sequences to the alignment.
Do not try too hard to automate every aspect of this… in fact it is quite common that you will have to manually curate parts of the process. Which is no different from the combined manual and automated curation of other reference databases, e.g. SILVA.
-Mike