There is too much detail here to deal with using just words. You need to draw a schematic with pen and paper , take a photo of it with your cell phone . Take a photo of you hardware and post the photos along with your code posted using the CODE TAGS "#"
tool button. We also need a SITREP on the hardware, (SITUATION REPORT) stating what is still working and what is "broken".
If the motor shield is ok (test it with a different motor) we need to know that. Get a meter and measure the resistance across your motor leads. I don't know if that will help but it may tell us something. Did you ever smell anything like burning motor ?
Remove the motor from the assembly and test it on a different output of the motor shield. (with nothing connected to the shaft if possible). Take voltage measurements across the motor when you test it.