Hi @Victoria92,
I'd suggest using qiime rescript get-pr2-data ... to fetch the PR2 files. This will download and parse and import the version 5.0.0 files for you. Then you can proceed as you've outlined. The upcoming QIIME 2 release should allow you to pull version 5.1.0.
Otherwise using SILVA would work too as it contains both 16S and 18S rRNA genes (SSU). You can also fetch the 23S and 28S (LSU) sequences too, check out the qiime rescript get-silva-data ... help text.
-Mike