The Key Dance or those cheap OBDII code readers only read out the Gov Mandated OBDII codes. There are hundreds, even thousands of other codes stored in the various modules on the vehicle that the manufacturers keep proprietary in an effort to force you back into the Dealerships and over pay for diagnostics and service. All the manufacturer's do this, NOT just Chrysler/Jeep.
OBDII is only what effects emissions, and just about anything going wrong with the engine will be the easy to read OBDII codes, perhaps a few transmission codes as well.
If the problem is NOT emissions, and your's sounds like it isn't, then only the dealer or a shop with an insanely expensive scan tool can read those codes that very well might be stored.
Your dealer should have used the Dealer tool to check for codes in the vehicle that you can't read. Since the manufacturer insulate the Dealerships from competition, isn't it any wonder they get worse and worse, and when customer come asking for diagnostics and troubleshooting, the dealership leaves their tools on the shelf and just start randomly guessing, replacing expensive parts on a guess?
You have the right level of brake fluid, correct? i.e. no leaks?
What does the brake fluid look like? I know the O.M. says the brake fluid lasts the life of the car, but brake fluid can easily go bad within 10 years and cause rust or gumming up in the system. Fresh brake fluid couldn't hurt. But likely if the rust or gumming up is bad enough to cause problems, fresh fluid is NOT going to fix it. Fresh Brake fluid is a preventative measure. I change it every couple of years or when the fluid gets really dark, I have never had to replace a hydraulic part of the brakes in any of my 10y.o. + vehicles for rust or gumming up internally.
You've done a visual inspection of the whole ABS system, no damaged wires to sensors or modules, etc?
Is the vehicle lifted, has oversized wheels/tires? Etc, anything that a mod could effect the suspension or the tire rpm relative to speed? Lots of people get erroneous traction control/ABS/Stability Control reactions after lifting and oversized tires. The new tire diameter can be programmed into the modules so they can do better calculations and NOT erroneously apply brakes.
If the only time the pedal is acting like a blown out master cylinder, is when the ABS activates, I also would suspect the ABS module, that opens/closes valves to release or trap pressure, or the pump that provides pressure when its needed.