On Wednesday, July 31, 2013, Mayank Tandon wrote:
That's a neat trick, and I definitely wouldn't have thought of that approach, so thanks for that!  

After I finished writing this out, I realized it was super long.  So here are the questions I'm asking up front, so you can choose whether or not to read the details.  Thanks!

1. How do I output the quality scores when converting from FASTQ to FASTA?

You can't, unless you mean converting a FASTQ file into a FASTA and matching QUAL file?

Peter