Hey there @Jennifer_Fouquier! I started back at the beginning of this thread and worked my way through, I have some ideas. So, the main issue was a Feature ID mismatch. I was just reviewing the Ghost Tree Tutorial and noticed a discrepancy between what you suggest there, and what @ihoxie has done here. By looking at the provenance for extensions_otu_map_90.qza, I noticed that this file was built using the extensions_cluster command in q2-ghost-tree, but, the input sequences were @ihoxie's FeatureData[Sequence] from q2-dada2! My understanding is that the extensions_cluster step should have used the FeatureData[Sequence] file sh_refs_qiime_ver7_dynamic_01.12.2017.qza, because that is the list of features @ihoxie is attempting to build the foundation alignment from.
As well, it appears that the Feature IDs are subtly different between the extension taxonomy and the extension sequences, @ihoxie --- the IDs in the taxonomy has suffixes after the Feature ID, which changes the entire ID, so even after recomputing the OtuMap, you will still have issues there.
TLDR: input files to this command are a bit of a jumble right now, I think if you get things in order you will be all set.