Hi Ryan,
you are doing the right things in principle. However, the branch length of the original reference phylogeny need to be reestimated to be in sync with the alignment distances. This is not necessarily guaranteed by Silva. SEPP’s developer explains what to do in detail in the file “sepp-package/buildref/README.md” of this archive: https://github.com/smirarab/sepp-refs/blob/master/gg/sepp-package.tar.bz?raw=true
Alternatively, you might want to use a pre-compiled version of Silva 12.8 which we provide via the conda package conda install -c biocore q2-fragment-insertion. The three files will be installed into your conda directory/share/q2-fragment-insertion/ref/.
You can also directly extract and download the files from e.g. https://anaconda.org/biocore/q2-fragment-insertion/2018.2.1/download/linux-64/q2-fragment-insertion-2018.2.1-py35_1.tar.bz2 they live in the sub-directory share/q2-fragment-insertion/ref/
Let me know if you need additional help,
Stefan