I have an arduino motor shield r3 being used by a arduino uno. I'm running a 12 volt stepper motor that is attached to a 32 to 1 gear reducer. I have the Vin pin removed and powering it with a 12 volt power supply. After a few minutes of use of the stepper doing 2600 steps one way then 2600 steps the other way the shield starts to mess up and act like it can't handle the motor. The main chip on the board after the few minutes of running is very hot, I actually burnt my finger slightly from just touching it for a second. Is there any thing that could be wired wrong to cause this, such as the stepper not being wired right? Or could it be the stepper motor and gear reducer is just too much work on the shield? Any suggestion what could be wrong would be very helpful thank you.
Without knowing the power draw of the stepper motor, there's nothing to compare to the motor controller's capacity. The listing on eBay does not talk about the power draw, either. It's quite possible the motor draws more power than the controller can deal with without additional heat sinking.
Get some thermal glue/paste and a good IC heat sink, and put the sink on the chip. That will cool it right down. And if it doesn't, then add a fan blowing across it :-)