Welcome aboard to the most advanced business computing platform, the i5 (formerly known as iSeries and AS/400). A lot to consider in this migration, i.e, zSeries computing is done in binary while iSeries is done in packed decimal. I would invest the time and money with IBM consulting or a 3rd party. (Barsa Consulting in NY, http://www.ccslink.com/conversion/index.jsp) It is easier working with someone who has done it numerous times. What was the main thrust to the migration? Are you using DB2 on the mainframe? Good luck.
I would forget moving to CICS/400 – it was always somewhat of an “orphan”. I’m not even sure it is even supported – I don’t think it is under active development. There are conversion tools that go straight from CICS to native COBOL screen I/O which is generally a far better option. The same vendors have JCL to CL conversion capability in their tools.
Batch mainframe COBOL to COBOL/400 is no biggie.
The binary vs Packed thing does not need to be an issue. Fields that are defined as COMP will be treated by the 400 compiler as packed whereas the mainframe would treat them as binary. Change all COMP to COMP-4 and voila – the job is done. Binary on the 400 is as efficient as on the mainframe (which is to say generally that it is not as efficient as packed for most math).
You would probably want to change to using packed rather than binary or zoned if you are using them – but the conversion tools often offer this kind of option.