Between reformat.sh (to get the fastq) and tadpole.sh (to assemble those into a reference) BBMap Suite may have you covered.

For the conversion of BAM to FASTQ, you can use Bamtools: bedtools bamtofastq [OPTIONS] -i <bam> -fq <fastq> (you can check the documentation http://bedtools.readthedocs.io/en/latest/content/tools/bamtofastq.html).

To make a reference genome you can get the consensus sequence of your reads using Samtools. It is going to be something like this: samtools mpileup -uf ref.fa aln.bam | bcftools call -c | vcfutils.pl vcf2fq > cns.fq (based on http://www.htslib.org/doc/samtools.html).

If you need a smaller genome in general to align your reads against to it, you can get a subsequent of the genome of your interest.