Hi, recently I tried to print out a piece in two different colored filaments. While the printer was still on I paused the print, raised the print head, then manually turned the circular extruder knob to remove the old filament. I then twisted in the new colored filament I wanted to print with, but when I hit unpause in the Repetier program, the extruder motor began twitching. Again while the printer was still on and the print was paused (because I really wanted the print ), I unscrewed the extruder motor and y-axis motor, then wired the extruder motor into the y-axis motor slots on the circuit board to see if there was a problem with the motor. The motor was able to turn properly so I plug in the motors to their rightful places sand hit unpause in the program, but had the same problem of the extruder motor twitching. After talking with some friends about what I did, I quickly realized that I should have done all this with the printer off. So I purchased a new extruder motor, thinking mine was ruined. After plugging in the new motor to the proper extruder port on the circuit board I brought up a test print on Repetier to figure out if it really was a motor problem. The new motor does the same thing the old motor does and twitches whenever told to move. After all this, I came to thinking that there is problem with my circuit board....

Now I am not quite sure what I should do: research the problem more and see if there is a way to fix the board (being that they are quite expensive), or simply purchasing a new board (only if there is no way to fix my current board).

Thanks for painfully reading through all this
Any solutions/tips would be much appreciated!

Oh I forgot to mention, I also tried hitting the reset button on the circuit board to see if anything new would happen. But no luck from that...

Generally, hot-plugging a motor (unplugging or plugging in the motor with power on) can destroy the motor driver, but will not damage the motor itself. It's likely that you damaged the motor driver. What electronics set does your machine use? If it's an integrated board, such as Melzi, then a repair would be very difficult without an SMD rework station.

Yeah, its a Melzi board.

Most likely the motor driver chip (the black rectangle under the screw terminals for the E axis) would need to be replaced. As I said, this would be quite difficult unless you have experience doing this type of repair.

Another option if you don't mind kludging something together, is to wire up an external stepper driver to bypass the integrated one. You would need to solder wires to pins 40 (E-DIR) and 41 (E-STEP) of the ATMEGA1284P, and wire them to the STEP and DIR pins of a Pololu driver (or similar), as well as providing logic and motor voltage to it. You would also need to tie the MS pins of the Pololu high or low for microstepping, tie the Sleep, Reset, and Enable pins high as necessary, etc. This wouldn't be particularly easy, but would probably be more doable than trying to replace the integrated driver chip. It would be best to reference schematics of existing controllers, such as Melzi and RAMPS.

Just for the future experiments: DO NOT manually move any axes while the printer is on! It is best you do not manually move axes even with the printer off, but with motor wires still attached to the board. If you have to do that anyway, move it very slow.
If you know how to do it, you can replace the driver chip on the Melzi. While it is not so complicated, it is delicate and requires tones of attention.

3Dmaker4U has some good advice. Of course you are going to have to move axes manually sometimes, and you don't want to have to unplug the motors every time. However, do move them slowly, as the motors will act as generators and feed back current into your electronics. The faster you move them, the more voltage is generated, and enough voltage will start damaging things.

Ok thanks for the info everyone, I'll see what I can do.