Thanks for the info @PatoUru! Good news, I think we can use an easier import/demux workflow that doesn't require you to run QIIME 1 scipts. Your data appears to be a good candidate for q2-cutadapt:
You can import and demux using cutadapt, which will be able to search your original reads for your barcodes. Please give that a shot and let us know how it goes! 
