you can use all of your hours with two exceptions. You mentioned PIC and DUAL. According to JAA there an only be one person PIC in the Aircraft. not Two so either you are the captian or you are not If you had an instructor than you were student. I solved this by logging allhours that i didnt legally need to be DUAL just as PIC. According to JAA at the bottom of you logbook.
PIC + SIC + DUAL + INSTRUCTOR = total time (so you also don't log PIC and Instructor at the same time).
Problem 2 SIM time.
JAA Simetime is not written up as flight time just in the colom STD sesion, also not int the PIC SIC DUAL colom. Keep in mind that SIM time in a LEVEL C/D sim can be used towards your ATPL
My advice just transfer the hours to the top of your JAA logbook, not the first line and dont mention transfer from FAA logbook. and use your e-logbook to sort out the PIC/ DUAL probem and corret this also in your i logbook. You might loose som PIC time but in the long run it's more important to have a correct logbook.
For the rest. Once you have over 1500 HRS and an ATPL nobody gives a ****. I have 8000 Hrs and with all the 14 jobs sofar never had to show my logbook.
Good luck