I'm not up on Lemon law in Florida, or anywhere else - but...
The "Auxiliary" batteries in Jeeps are pretty notorious.
As I understand it, the auto start/stop function can pull the main battery voltage to low for the ECM and other electronics. The Auxiliary battery is a small capacity battery wired in to maintain the voltage for these electronics.
My understanding is that the OEM Aux batteries are on the crappy side and the electronics are poorly done, so the failing aux batteries cause all kinds of electrical issues.
If that car has repeatedly sat long enough to drain both batteries, they are likely damaged beyond recovery. (Thus they were replaced by the dealer.) Aggressive charging and jump starting could easily have damaged electronics, especially the notorious "Power distribution center".
I don't do Jeeps, but my coworkers and friends have educated me on these issues.
I have jump started several and helped change one power distribution center.
Sadly, while the batteries and electronics are notorious, it sounds to me like these issues are on you for letting the car batteries go dead. With keyless entry and keyless start and all the other "features" in these modern cars, they just drain the battery when they are sitting for weeks.
Regarding alignment - again, continuous alignment issues seem to be a feature with Jeeps. To happen in a few hundred miles - if it didn't hit a curb, loose parts from the factory would be a good guess. but nothing to do with the electrical issues.