Is my RNA-seq experimental design correct to use it for SNP calling?
Using RNAseq for SNP analysis is not the best tool available for several reasons. First, you will only find SNP in genes that are expressed (you need more than 120 reads per SNP in your experiment). Second, you will only find SNP in coding regions of the genes. For your particular experiment, where you have a pool of 60 individuals per sample, it's another drawback because you'll have 120 alleles in your sample (without knowing the allele combinations of the individuals).

Of course you can still try to find SNPs that are present in your phenotypes, but real GWAS kind of analysis is in my opinion not possible.