When I press the brake pedal the brake lights flash, under two circumstances 1) while the turn signal is on and 2) when the headlights are on. The rear fog light indicator on the dash also flashes at the same time. Also if I turn on the hazard lights there is the loudest clicking noise that sounds like it's coming from the gear shifter. Possibly unrelated but it did start shortly after replacing a bad headlight bulb.

 

vjcoiktn, it is sounding like you have a ground wire issue with one of the rear tail lights. I would recommend removing both of the rear tail lights and unplugging them. When you unplug the connector, look for a dark/charred spot on the plug to see if you have a wire that got too hot and has shorted somewhere.

With both tail lights unplugged, try the turn signals to see if the problem has gone away or if it is still present. If the problem is still there, then you have a problem with the wiring harness of the car and will require either a fair amount of electrical knowledge to go through the harness of the car or to be taken to a shop to be evaluated/repaired. If the problem has gone away, then you have a problem with one of your tail lights. At this point, plug in one of the tail lights (which one doesn't matter) and see if the problem returns. If it does, unplug that one and plug in the other to see if the problem is common to both or just the one. Normally the problem is just the one tail light.

Once you know what tail light is giving you grief, remove the back of this tail light to expose all the bulbs and remove all the bulbs. Check to see if you are still having issues. If yes, then the taillight backing plate is bad and you will need a new backing plate/tail light assembly. If things are still good, start putting the bulbs in one at a time (ensuring they are properly seated) and see which one causes the problem to return. If the problem returns, remove that bulb and continue installing all the other bulbs. If it appears to be isolated to just one bulb, ensure you have the correct style bulb that goes in that spot and also do an inspection of the contacts inside the bulb base to make sure that they are not touching and/or loose. If they appear to be bad, then odds are you are going to need a new backing plate.

If you are still having issues, let me know and I will assist however I can.

 

Thank you for your quick response. I have unplugged both tail light assemblies. There is no loud clicking when the turn signals or hazards are turned on and they appear to function normally (front only of course). Plugging either of the tail light assemblies back in causes the issues to return. I tried each separately. There is damage to the same pin/slot on both sides. It is the second pin (going from the center of the trunk toward the outside of the car). Additionally to aid with the diagnosis of the problem...when the headlights and turn signal is on and brake pedal is pressed, the brake lights flash including the third one.
With just the turn signals and nothing else activated they function normally on both sides. The rear fog light indicator does initially come on but then goes off.

With the turn signals and headlights on only all of the brake lights flash including the third one and the correct turn signal flashes.
With just the reverse lights on the rear fog light indicator does stay on. When depressing the break with the reverse lights on the reverse lights dim and the brake lights on the tail are rather dim as well. The third brake light is normally lit.

With only the brake pressed the rear fog indicator light is constantly lit.

I have done a fair amount of mechanical and electrical work. I suspect whatever connects to that second pin is the culprit. I'm going to start looking for a schematic to see if I can start to trace it to the source. Any input you have to offer is much appreciated.

 

It still sounds like a ground problem to me too. It is looking for a ground (-)any place it can find one. Find the wire in the back that is the ground and then add one of your own ground in with it. Now what happens?

 

is the ground located in the harness if not where would i find it

 

Im curious to know if you found a way to fix this issue cos im having the same problem. About a year back i had replaced the whole xenon front light portion and one brake light in the rear. The issue started only after that and the shop who did the wiring nor the agent was able to correct it!