I agree that your workflow is indeed comprehensive and well thought. some additional considerations to add to those stated by David:
i would consider setting a lower limit for SNP inclusion (less than X30). you should be mindful that setting a higher lower limit was shown to decrease sensitivity without a substantial gain in specificity and should be considered in your specific experimental context.
comparing your called SNPs against the dbSNP data base is also considered good practice, if the proportion of novel SNPs in your data is suspiciously high (>10% in coding regions), you should consider setting a higher quality bar.
SNP calling quality could also be assessed by checking the Transition/Transversion ratio which is expected to be around 3.3 in whole exome sequencing.