Have you given any thought to the idea that the main computer is toast?
Your car runs poorly, it MUST BE THROWING CODES. It has to be. If you cannot pull codes, then at least one of them is that the computer doesn't work, and if there is no computer then the car should be expected to run like crap.
Your car is a 2001, so it will talk to through the Data Link Connector to a pc running the diagnostic software. Your car _should_ communicate through the OBD II data port in the left side footwell, but you have said that it does not. You confuse me on this point though, you said it powers the scan tool, but then you said you can't find 12V. I'm confused at how the scan tool can be powered without 12V. You MUST set the ignition to RUN (Position II) to get codes out.