Hi Matt! Sorry for the delay here!
I haven't had a chance to remove the extra taxonomy classifications and am kinda swamped this week with a big deadline Friday but its on my "to-do" list for next week to finish formatting this. In the meantime, attached is a link to the taxonomy and fasta files at the point where I currently am in case using the files in QIIME2 format is time sensitive:
RDP OTU fasta file
RDP updated taxonomy file
If you figure out how to remove those extra taxonomy labels in the meantime and don't mind sharing the code, I would be grateful! Otherwise, will continue working on this next week. Let me know if these don't work for some reason!
Katherine