The very, very first thing to do with any electrical problem on a YJ is check the grounds. In your case check the headlight grounds first. There's a screw near each headlight on the engine side of the grill panel. They will have a black wire with a ring terminal running to them from the headlight plug.
Take the screw out and sand or scrape the area where the screw attaches to clean, shiny bare metal. Put the screws back with the wires and a dab of dielectric grease.
Also, check the ground strap from the back of your engine to the firewall. Then check the (-) battery cable where it bolts to the block. Take each ground apart, clean where they connect and put them back together with a dab of dielectric grease.
If cleaning the grounds doesn't fix the headlight pulsing, dig into the following. Other posters have discussed this in the past. I have a different type of alternator and charging system than you have but this is what I remember.
Your alternator voltage is controlled by the PCM unless you have an aftermarket voltage regulator.
Is your check engine light lit? If the voltage regulator within the PCM goes bad, you can buy an aftermarket voltage regulator. Sometimes with an aftermarket voltage regulator the PCM wants to see voltage from the alternator. If it doesn't see the voltage, the PCM will throw a code.
Pulsing headlights are a sign of poor grounds or an aftermarket voltage regulator that isn't wired properly or might be failing.
Hopefully other posters with aftermarket voltage regulators can chime in and give you more and better advice.
It could be something as simple as a loose plug. Check your connections.
Wow! You guys are good!!! Yes i have leds (tail lights) yes i have external voltage reg yes i have check eng lite codes # 21 41 46 i think? YES I will check grounds !! I will keep you posted Thanks again Tom
21 - 02 sensor input voltage stayed above normal range
46 - battery voltage high while charging
41 - alternator field control circuit open or shorted.
To clear the codes disconnect the battery touch + cable to - cable for 30 seconds reconnect battery.
Is your external VR connected with a relay? If not you need one. and it should be wired like this
Terminal 30 to battery
Terminal 85 to ground
Terminal 86 to ASD
Terminal 87 to VR
This should clear up your pulsating lights.
A field replacement module should keep the obd code 41 from returning
My voltage regulator was going wonky in my pcm on my 93 YJ. I did what was mentioned except, I ran a relay to power my voltage regulator, not my headlights. Works like a champ!
My check engine light did not come on after I disconnected the wiring from the pcm to the alternator, so I did not Have to instal a field replacement module.
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