Possibly shorted MS unit?
 

So the other day I was driving and my ghetto rigged battery shifted in the trunk and negative terminal connector melted to the metal of the trunk. I got a new terminal and even tried to jump the car, making sure it wasn't the battery. I know I am getting power as my gauges illuminate but when I try to crank the car all power is lost. Also, both the wideband and boost gauge flash like they have been reset. I tried to hook up the laptop and connect it to tuner studio but I think the car has to be running for the connection to happen? Any help would be appreciated.

I would first make sure the MS is getting good power with the key on.

if your ignition is on your laptop should connect to MS.