First off you're not comparing same brands. One site has Stainless Works which is fine engineered and American built and you're comparing it to eBay Chinese made JUNK! Then you have to see if the JBA midpipe fits the China JUNK headers. Usually manufacturers make headers and mid pipes to fit...
It's more of a look. I have the original FR3 handling pack with the 1.5" drop and the car looks great be-it not the greatest over bumps (ouch) the reason I got it is because over 100mph the nose of the car lifts and stability is strictly stupid. You have to make final decision.
Have you checked engine and/or trans mounts? You don't rest your hand on the shifter when driving do you? That can crush the NVH bushings in the handle base.
Outside of body trim there is nothing real special about a California Special. Outside of a slight HP bump with the Coyote why get rid of something that you know how well it was maintained and treated etc...
The difference is the sway bars, they are different because the fatter bars from coupe wont fit with the X brace for the missing roof. I'm assuming the front is different too to match better with different rear.
The differences between the engines are intake manifold which you can just swap from yours and the cylinder heads but if you just purchase spark plugs and ignition coils for a 2010 you'll be fine, other then that its a drop in.