BWA expects mate-pair F3/R3 (as input to solid2fastq.pl).
You could reverse-complement your F5 reads (and reverse the quality) and send them to solid2fastq.pl and it should work more/less as expected. Then you just have to consider how having the low-quality bases at the start of the read affects BWA (lh3?) -- you may want to quality trim your reads before-hand.
EDIT: if this works, it would be just reverse, not reverse-complement of the F5 reads.