Hey @Vixer!
Perfect, then you don't need a fastq file for each sample, rather the fasta file you get from qiime tools export should be sufficient, since your interest is how taxonomy gets assigned to each sequence, the particulars of how many and which samples they belong to isn't relevant.
This is the part we don't have a great answer for, as you will need the feature-table and the taxonomy. There's another thread exploring Krona, but I don't think it made it to a final solution.