Prusa i3 Dual Extruder Setup Issues
Thanks to the comments, I was able to narrow down the specific issues in the firmware. The firmware version was really out of date, so I recommend finding the latest stable version.

Therefore, I found the latest stable version of Marlin, downloaded it, and created my own edited version. I went line by line in configuration.h and configuration_adv.h, with the old version I had side by side to the newer version, making any and all appropriate changes. Below are the lines I found most important to evaluate when setting up a second extruder.

Make sure the you have the right board selected from boards.h:

#define MOTHERBOARD 34


Make sure the # of extruders is specified:

#define EXTRUDERS 2


Make sure the sensor is active:

#define TEMP_SENSOR_0 6
#define TEMP_SENSOR_1 6
#define TEMP_SENSOR_2 0
#define TEMP_SENSOR_BED 6


This should be considered:

#define HEATER_0_MAXTEMP 240
#define HEATER_1_MAXTEMP 240
#define HEATER_2_MAXTEMP 240
#define BED_MAXTEMP 90


Everything under this comment should be looked at:

// Preheat Constants


These would allocate the second extruder for other motors:

#define Z_DUAL_STEPPER_DRIVERS
#define Y_DUAL_STEPPER_DRIVERS
#define DUAL_X_CARRIAGE


I'm sure there are other parameters I may have missed, and these are specific to my Prusa i3, but I hope this helps out anybody else in the future.