I just wanted to write this up to help anyone that encounters the same symptoms.
I started my Jeep yesterday evening to come home from my kids fair and I noticed that there was now a loud, rpm dependent, whine from my alternator. Since I had about 15 miles to go, I basically just drove the quickest, most direct route home. All the way home, my Jeep drove like normal, with the exception of the alternator whine.
When I pulled into my neighborhood, suddenly the ABS and Traction Control lights came on and this constant high-pitched beep started. I also noticed my acceleration felt like the transmission was slipping and the engine was surging. I had to put my transmission in Park before putting it into reverse to back into my garage. Even after I turned off my Jeep, the high-pitched beep did not stop. I had to remove the negative battery cable to get it to stop.
This morning, I removed the positive battery cable and the alternator. I took my alternator to O'Reilly and obtained a new one. When I got it home and put in on the Jeep, upon startup, it started making a chattering noise that sounded like the bearing were bad. So, I had to take it back to another O'Reilly to get a second alternator from them. This one actually worked.
2009 Jeep Commander Sport 3.7L V6
Upgrades: K&N Filter, DRL's, Rear Handles, Curt Hitch, Steel Suspension Skid Plate, Fogs, Secure Console Cover, Bilstein 4600 Shocks (F/R), Moog Front/Rear Swaybar Links, Moog Front Swaybar Bushings, Moog Front Lower Control Arms, EBC Greenstuff Pads, Ignition Mod