Ok so I went to auto zone and ran the code.
It turned out to be a P0113-IAT Sensor 1 Circuit High Input. I cleared the code and all has been good since. I asked the guy at auto zone about the IAT sensor and why it would have went off. He said that more then likely it was a "hick-up" signal since the code cleared and since what I did should have had nothing to do with the new alternator. I am glad about this!
graniteguy- i don't have a voltmeter, but I am going to try and find somebody with one and check to make sure everything is working good. I turned my truck on and off a ton of times since I put it on and no issues, so I figure it is working good.
Jacob 2002 Extra Cab 3.0L v6 XLT w/3.73 gears Automatic Bright Island Blue K&N Fipk, Alpine 9815, Memphis components, Hood Struts, Auto-Down, Reverse Glow Gauges, white HVAC gauges, Radio On MOD, EDGE bumper, explorer radio bezel, Blue LED: Headlight switch, CC, and both Fog Light Switches; OHC, Auto-Dimming mirror, Acetoned badges, Keypad Mod, Tailgate lock, Bed-Extender, Under Drive Pulley, Hidden-Hitch, 60Ft. 67,000lb Strap, 2001 Explorer Limited seats, 3" Spindle Lift, 2" blocks, Bilstein Shocks, American Racing Diamond Back Chromes 15x8's, and BFG 31's
Plus MUCH more…