If you have only a small number of jobs to migrate, consider migrating them all at once, perhaps over a weekend. With this approach, you can first run your customized migration utility against each set of input statements that needs to be migrated. Your migration utility would read the existing statements defined as input, and write the equivalent CICS BAC command statements to a new file, in a form ready to be used by the CICS BAC batch request utility. When you have created the equivalent CICS BAC commands, you can then update the JCL for each job, converting it read the CICS BAC commands file as CBKIN instead of the existing input file.
However, this approach is probably only suitable for a small number of jobs that you can handle in this way over a short period of time.