My 99 civic ex is running totally on battery power. the alternator isn't charging the battery. I cannot see any shorts in any of the lines, or any blown fuses under the fuse box. I have replaced the battery, and the alternator belt, and even put a new alternator in from autozone.

the old alternator tested good, with amperage difference of only 5 percent, according to the guys at autozone. the new alternator makes my electrical pulse like a strobe light, to the point of not being able to drive it at night. i read an old thread with the same problem, the solution was a short in the wiring under the intake manifold. I have looked at all wires coming through the area, and cannot see any damaged wires. I put the old alternator back in, which like I said, tested good, so as to not have the vehicle pulsating. I am at my ends wit.

is there another power regulator that would cause this, besides the one voltage regulator inside the alternator? or is there anything else that would impede the power to get from the alternator to the battery?