Not sure if these are related but I'll go ahead and list them...

Dash lights, headlights, AC, radio(pretty much everything but the engine) will turn off and turn back on. Sometimes the Clock will reset as will the Drivers information and radio presets, other times not. Sometimes the car will even die if the car is just idling. Seems to occur when the radiator fans(high ones, lows don't work at all. Resistor is in the mail) turn on.

Last night car had to be jumped. Battery was tested today. 100% fine. 583CCA and 12.6 Volts. When it had to be jumped the dome light was flickering like a strobe light. I assume this was due to the battery being dead as it works fine now.

Passenger side Headlight sometimes doesn't turn on(or goes out?) turning the lights off then back on seems to fix the light.

I bought the car used a little over a year ago. Had an aftermarket CD player put in and also replaced the coil in the A/C Compressor.

Normal diagnosing I can usually due but electrical stuff and I absolutely terrible at. My next stop is getting the alternator checked. Anyone have any idea where I should go next?

 

Flickering lights CAN mean a bad diode in the alternator...
BUT the things you state makes it sound more like a bad ground...

So check the MAIN ground wire next to the PAX side engine mount...might be a cheap fix if it is loose or corroded.....Would account for ALL your issues.
next...check the ground by the battery (in the trunk on the S)

 

PAX side = Passenger side?

I also came across a thread from earlier this year and the Body Control Module was suggested as an issue. Is this possible?

 

Year, model and miles go a long way toward helping identify possible problems/solutions. A tedious search thru previous posts will point to mysterious and multiple malfunctions as being related to a failing battery. The ECU becomes psychotic and throws out all sorts of warnings.

 

2003 Mini Cooper S. 122k Miles. Battery is fine its less than a year old, just had it tested.

 

Yup...pax short for passenger
Might be...the bcm...
But try to eliminate the simple/cheap/easy stuff first....
The bcm is the most $$$ possibility....so IMO check other stuff first...grounds, etc
Ever have any moisture/water issues in the car? Folks with bcm issues often have had water leaks, etc...getting the unit wet...it is in the area of the passenger sidewall interior wall..by their feet.

 

No water issues. Carpet is dry and I cant see any evidence of water in the foot well.

PAX ground looks good.

Still need to get the Alternator checked.

Should I go ahead and get to the BCM and check for corrosion or water damage around the BCM?

 

my car has very similar problem, although mine is a base model 2006 with 60,000 miles. I would be very interested to hear how you resolved your problem? Thanks!

 

Not likely. But an aftermarket stereo poorly installed can cause all kinds of issues. E.g. ground touching hot. Check the back of the radio. You never know who did the install and if it's botched.

 

Agreed. Im gonna pull my Radio this weekend and check out the radio install(I didnt do it myself.....maybe I should have....)

My issue is very infrequent. It rained recently and I kind of hoped some issues would crop up but nothing has as yet.

BCM seems to be where Im headed. When I pull my radio I will also pull the BCM and check it out.