First, are your battery cables frayed at all? Specifically look at the negative (ground/black) cable, it should go from the battery to the firewall and then down to a bellhousing bolt on the trans. If any of the connections are frayed it can give you problems.
Also try disconnecting the factory security controller. It's right near where the ecu is, behind the pass. side floorboard. Here's a pic:
If your car's an auto, make sure its fully in park. I know it sounds stupid but I've done it before. Don't ask...