Only 2 two taxa from 18S taxa barplot

The differences in ranks between 132 and later versions has to do with our improved parsing. I would not use 132 anyway as it is old. For a historical point of view for the 14 ranks please read this post. Many of the recent versions of QIIME 2 make use of RESCRIPt to prepare SILVA. You can also do the same yourself as outlined here.

I am not sure why one of your taxonomy files has truncated taxonomy.

I'd stick with later versions of QIIME 2 and SILVA (138.1). Again, you can curate the SILVA database yourself too.

I do not think these are the correct files. I do not see where you ran rescript orient-seqs in your provenance.