Fixes to Intra_substitutionS_isomerization family

Fixes to identical groups for parent and children by making parents more general:
- SJ and SsJ
- SJ-3 and SsJ-3

Fixes to S-Cs(CtHH)C, S-Cs(CtCsH)C, S-Cs(CtCsCs)C groups which did not properly
have Ct groups in them.