I would start by doing as much research as I could at some of the IBM sites such as the iSeries Information Center. Yes, I would start with a Full system save from the old machine, but I would not do a Full system restore on the new machine. You will want to take advantage of some of the new features available to you in V5R4. Hopefully you will have time to do testing on the new machine before having to do the Final Cutover. Not knowing how complicated your current setup is makes it hard to make anything other than general suggestions.
If you have purchased your new system through a Business Partner, they should be ablke to help you out much more than any of us as they can get into the details of your current environment.
The transition should be exciting as you have the opportunity take a giant leap forward !
Hope this helps, Bill

I have done these in the past. It is important not to change the installed V5R4 Operating System or put any of the old system librarties onto the new machine. SAVLIB Usrlibl and exclude QGPL and QUSRSYS. Also Save Security Fata. Restore Security Data with the new option for User profiles and *PWDGRP for Security Data to put profiles from old machine onto the new machine, then restore User Libraries to new machine, SAVE OLD QGPL and QUSRSYS and restore to new libraries on new system I usually make QGPLOLD , QUSRSYSOLD. Then using STRPDM copy User objects such as Output Queues and Files in QGPL OLD/QUSRSYSOLD to QGPL/QUSRSYS. Then do User IFS and QDLS Objects from OLD to New. Finally do a RSTAUT. Manually redo WRKJOBSCDE if any. Reminder unless you use BRMS or 3rd party software Spool Files will not come across. I have used OPS Nav with some success to move between boxes......Rick