Well, if you can reprogram it easily with the mpguino circuitry unplugged, and it works well with it plugged in to the car, then that might be a workaround.
I guess I would plug things in one at a time and see when the usb starts flaking out. Buttons, interface circuit, LCD.
You need an isp cable to load bootloaders, and some patience. I made an isp cable out of an old parallel cable and a few resistors and a bit of hard drive connector. I've revived a couple chips with it and can buy plain atmega168 chips without a bootloader on them. But if your arduino returns to "normal" without the extra circuitry then the extra circuitry is suspect.
