I think that the best route to go, is to regard P3Dv4 as a totally new sim, which it actually is. Keep your 32bit add-ons for your older sims, & populate P3Dv4 with add-ons that are written & optimised for 64bit.
Do not try & bother to migrate & shoe-horn older 32bit add-ons into a 64bit program, you WILL be disappointed. Your older add-ons are obviously not optimised for 64bit, & probably will not work as they did within the older sims.
In any case, the price of a brand new P3Dv4 is probably the price of a decent add-on, or two.
If you want to go cheap, go for FSW! (or stick to FSX)
You ask.. 'Lastly, if one was to use both P3D and FSX on the same rig, would there be a preference for flying GA on one and military (mostly Naval Ops) on the other format?'
It will obviously be your personal preference to do whatever you want to do, with whatever sim, with whatever add-ons are available for that particular sim!