Appreciate the feedback everyone!
So far I have one FAA compliant paper logbook, one JAA compliant paper logbook, and a JAA compliant electronic logbook. My initial plan was to transfer all FAA hours into the JAA paper logbook, as well as logging every flight (FAA+JAA) in the JAA electronic logbook. I've removed my PIC time from all Dual flights in the electronic logbook, meaning that PIC reflects JAR definitions. The only loss I'm making is 100 hours of PIC time. The totals will be equal. IFR is a tricky one, but I'm pairing actual + simulated from the FAA logbook and adding that to the IFR column in the JAA book. Apparently the NCAA wants this to be flight plan time, although JAR-FCL specifies the IFR-column to be "simulated and actual." So, seems to be somewhat open to interpretation.
I could transfer PIC-time as-is, which would reflect reality, but I'm unsure if I can defend 1. Non-JAA recognised PIC time in the JAA logbook, and 2. An electronic JAA logbook specifying my instructor as Commander, but me logging PIC-time.
Another issue is the FAA "Dual given"... probably shouldn't be transfered to the "Instructor" column in the JAA logbook, huh?
This might be one, big unnecessary headache, but I've been trying to clean up my intercontinental logbook mess as correctly as possible. Want to be cocked, locked and ready to rock on the paperwork before submitting those applications!
