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Hey I've been having a bit of charging problems with my civic and its making me crazy

So to start off its a 2000 civic SI originally had a b16a2 from factory. It now has a 96 spec JDM type r with the matching p73 ecu.

It has a obd2b to obd2a conversion harness and I have no CEL.

When Im driving around at night time my headlights will go dim and I will have a loss of power. So I decided to run two wires from my battery terminals and to a multimeter. When I first start the car from a cold engine the volts read around 14.xxV then as the car warms up and just driving around normal the volts will go between 14.xxV and 12.6xV I just put a brand new alternator in and its still doing the same thing I also tried driving around with the battery unhooked to see if it possibly is causing a short and when I turn the headlights on the car almost dies. Then with the headlights on when I came to a stop the car died.

What can be causing this? I have checked and replaced my grounds also. Any ideas? I have also recently checked my whole wiring harness for shorts. What else in the charging circuit could be causing this?

 
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I'm really not sure...but you are describing my problem to a T. Did you ever find out what was wrong? I have a 2000 Civic Si, but still have B16a2 motor. I have a turbo timer with battery meter. Mine goes up and down between 12.2 and 14.1 volts. Recently, it will cut off while I'm driving down the road (have to push in the clutch and restart it while driving). I took it to an import shop and they said the alternator was bad, so it was replaced. I also have a new battery on it. After two days of working fine, my car started going back to the same unreliable charging problem. This happened about two years ago, and the shop replaced the entire wiring harness because the turbo was too powerful and cracked the motor mounts, which in turn pulled on the wiring harness and caused shorts.

Anyway, is your car back to normal? What did you do to fix it? Thanks!

 
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sounds like a bad battery! have you had a load test done on the battery? that would reveal if the battery is still good. you see the way the most charging systems work is the alternator usually only supplies the battery with amps. most on the cars accessories run off the battery, the alt general helps out when demand exceeds the battery's ability. eg: lights, wipers, heater, sound systems with subs... with a bad battery the alt will be running within at least 10% of spec for it (100amp alt = 90amp output) so do the simple things before replacing parts.
good luck