1995 Neon, 4cyl, MT isn't starting, what could be wrong?

You covered just about ALL the bases here but you did not mention if you have injector pulse? (the actual ground signal from the ECM that fires the injectors) To check this you need to see if it will run on alternative fuel (this is best tested with a can of choke cleaner and spray a liberal amount into the air intake hose and crank the engine to see if it fires! If it does than you have no pulse.(the 12 means that the battery was disconnected)