Getting fastq files for submitting to SRA

I have done quality check as described in the MiSeq SOP, which means that the length of sequences do not match the length of the .qual file anymore (because of the aligning and screening to the 16S region that was used). How can I trim quality file to the same length so I could merge fasta and qual back to fastq and submit to ENA SRA database? Or do you usually submit raw data (without barcodes and primers) before any quality check has been done?

Submitting the raw data would allow others to follow your analysis or run their own.