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I had some issues when my Fuel Pump relay wires touched on the connector touched each other due to being stripped back from the connector too far. Dont know if this is it,,,,,
Alternator is easy enough to get checked out and is free at most parts stores, but I think you probably have a loose ground somewhere. I am experiencing the same problem here and I am convinced it's just a short somewhere or a loose ground. Not sure though the location of each ground or how many I need to look for.
Most likely your alternator voltage regulator is oscillating and parts stores have no means to check for this. Proof is by unplugging your alternator with the engine running and seeing if the flickering stops. Or, better yet use an oscilloscope across the battery with the engine running and observe the amplitude and frequency of any alternating waveform on the battery.
Ahhh....work flashbacks. I doubt an o-scope is part of very many amateur mechanic's tool box.
My car did the same thing when I put one of the higher power accel cap/rotors in the car. Put a stock ac/delco cap and rotor in it and it's been fine since. For some reason these cars are kinda sensitive to electronics.
Get a multimeter on the outputs of the alt and see what kind of voltage it's puting out there. You can also check the voltage accross the battery. If you use an analog multimeter, you should be able to see the fluctuations JFB is talking about, but obviously your not going to be able to measure it like you would with an o-scope. Normally, you should see a constant voltage accross the battery.
If you unplug the alt and the car runs the same or better, it's probably the alt. If it runs worse the alt's probably not your culprit.
Did you do anything to the car before it started happening?
I tuned the car up, but it was flickering when I purchased the car. I am going to unplug the alt and see if that is the problem. I will keep you posted.