Hi, @perdita!
Please correct me if I am mistaken, but it seems to me that the only relevant portion of this diagram is the upper left corner which shows that the 454 Sequencer generated .fna/.qual files. Given that you have the .fna/.qual files, and no* the results of the rest of that analysis process (right?), I don't think the rest of the diagram is relevant. Does that make sense or am I missing something?
It appears that the question is not so straightforward. Please see this discussion on biostars.
I need to do a bit more research to answer your other questions confidently. But elsewhere on the forum, people have discussed importing this type of data using a manifest file. For example, see this post: Importing 454 data to run dada2 denoise-pyro - #3 by Mdavrandi
You might also look into using q2-cutadapt for demultiplexing if required.
Also, depending on what you need to do, you might have other options.