Hi @paperwolf,
Is there a reason why you simply did not use the SILVA SSU classifier? Remember 16S and 18S are homologues and can even be aligned together in the same alignment. Which is what SILVA does. I'd recommend following parts of the SILVA tutorial, and simply use the SILVA SSU reference database to classify your reads.
To extend what I mentioned above, I am betting good money 
that all those unclassified reads are actually bacterial 16S rRNA gene sequences. 
The V4 primer will amplify both 16S and 18S rRNA gene sequences. Because you have no bacterial sequences sequences in your reference database, they will be returned as unclassified.
Even if you only care about 18S rRNA gene sequences, you should always make sure you have outgroup taxa, i.e. bacteria in this case, so you can identify and remove these unwanted taxa.
You can also combine the outputs of this GenBank tutorial with your 18S rRNA gene sequences, and then train that as your classifier. But again, I'd sanity-check with a SILVA classifier first.
-Cheers!