I'm not sure I'd blame the harness mod yet, there are other easier tests. The BCM calls for brake lights for lots of weird reasons. It's been months since I've worked in this, so the memory (nightmare) is getting a little foggy. Is your third brake light hooked up? Do you have resistors in the system yet? If you have low power draw at the brake lights, the BCM will call for brake lights. Are you using a different pedal box than the one that came with the car? If the brake position sensor (BPS) isn't calibered correctly, it will throw brake lights. There are a few other items as well. Are all of your grounds making good ground? Does your car have a brake fluid level sensor? Is the reservoir full? If I remember correctly, the cruise control system is tied to brake lights as well although I don't remember the relationship. Do you have abbi-directional scanner?