Just an update on this. The most basic solution was just combining the barcode files in Qiime1 as per the "Two index/barcode reads and two fastq reads" instructions and then importing them into Q2 using the EMP-PairedEnd protocol after gzipping and renaming the fastq. files
In case this helps anyone else reading this, the structure of the files were:
_R1 <- forward reads + qual scores (barcodes and adapters removed)
_R2 < forward 8nt barcodes in the same 4 line format and order as R1
_R3 <reverse barcodes as above
_R4< reverse reads same as _R1
Using Qiime1 v1.8
extract_barcodes.py --input_type barcode_paired_end -f _R2.fastq -r _R3.fastq --bc1_len 8 --bc2_len 8 -o parsed_barcodes/
In talking with the sequencing facility they think that this should be a compatible format in Qiime2 since its a very common way of receiving the data from various facilities, especially as it was previously compatible in Q1.