So after doing a bunch more research and talking to some more people it appears the right way to setup the coil-rite bags on a TJ is to leave the bump stops in and make sure the bag height is shorter than the level spring gap but long enough to act as the lower bump-stop pad. To work this out you need to take the level spring gap to the bump-stop cup with all bump-stop spacers removed (about 11" in my case), then minus the up travel you need/want (4" in my case) plus up to 1 inch for bag depression when the bag is acting as the lower bump-stop pad (dependant on bag PSI). This means with my 4.5" synergy springs I need a bag that is approximately 8" long and a little over 5" in width. You definitely want to put the jounce back in after measurements as this protects the bag from the cup and adds further dampening when you hit the bump-stop which combined with the bag apparently gives a similar overall effect as a hydro bump stop (note I said "similar" not the same).
Reading a lot of reviews it seems like the firestones are the only way to go, they are a much thicker bag and are backed by a lifetime warranty on the bag itself, I will probably put the bags in kevlar sleeve to help protect them a little further or possible carry an extra bag when doing long trips in the middle of woop woop.
Taking everything into account above it appears the Firestone
4172 bags are the perfect size for my needs, no plastic spacers will be needed and should give me everything I want as far as travel and support goes. I could run the 4175 bags and run longer bump stops (add 2.5" on bump stop extension) but I would imagine the more spring that is filled with the airbag the better the control you will have over the spring rate and therefore a better overall ride quality.