I had a similar problem with my Tacoma. I ended up grounding everything I could; battery to frame again, ignition, fuel rail/injectors, alternator, and multiple chassis grounds. I went down to autozone to swap out the spark plug wires, under warranty, and when I wiggled the first one loose in the parking lot, it was hot. So I plugged it back in and was gonna change them at the house. On the ride home I didn't have any more engine noise. I swapped them anyway and made sure that they were properly seated and not causing any more noise. FWIW.