Electrical power comes from the battery to the engine compartment via a thick red cable routed on the right side of the car. That cable terminated and joins another red cable at the jumper post located under the red plastic cover under the hood. That second cable goes to the starter and the alternator. So, disconnect the ground cable from the battery and disassemble the jumper post. It’s basically a large bolt onto which the 2 cable lugs sit. Make sure the lugs are absolutely clean. Reassemble and reconnect the ground cable at the battery. See what happens.

What brand is the alternator? Be advised that BMW sourced alternators from Bosch and from Valeo. They are not interchangeable without some work. A genuine Bosch voltage regulator (VR) will cost about $50 at FCPEuro. Make sure you buy the VR for the amperage rating of your alternator. It’s either 90 amps or 120 amps. Check the label at the back of the alternator. You’ll also need to buy the alternator’s rear air cooling duct as it’ll crumble when you take it off. Go to www.realoem.com and enter the last 7 characters of your car’s VIN. Hit enter and bookmark the page. Scroll down to engine electrical and find the alternator that’s in your car, again by amperage rating. Item #3 is the cooling duct.

Please report back with the results.

 

Electrical power comes from the battery to the engine compartment via a thick red cable routed on the right side of the car. That cable terminated and joins another red cable at the jumper post located under the red plastic cover under the hood. That second cable goes to the starter and the alternator. So, disconnect the ground cable from the battery and disassemble the jumper post. It’s basically a large bolt onto which the 2 cable lugs sit. Make sure the lugs are absolutely clean. Reassemble and reconnect the ground cable at the battery. See what happens.

What brand is the alternator? Be advised that BMW sourced alternators from Bosch and from Valeo. They are not interchangeable without some work. A genuine Bosch voltage regulator (VR) will cost about $50 at FCPEuro. Make sure you buy the VR for the amperage rating of your alternator. It’s either 90 amps or 120 amps. Check the label at the back of the alternator. You’ll also need to buy the alternator’s rear air cooling duct as it’ll crumble when you take it off. Go to www.realoem.com and enter the last 7 characters of your car’s VIN. Hit enter and bookmark the page. Scroll down to engine electrical and find the alternator that’s in your car, again by amperage rating. Item #3 is the cooling duct.

Please report back with the results.

Trunk side wiring is fine, sits snug, no corrosion present, will have to remove b-post side cabling and check it. Alternator is 120A Bosch with 3 pin voltage regulator with rectangular plug, seems to come from junkyard prefacelift E39\E46 MY is 1999, it was on the car when I bought it 2 years ago. Bosch voltage regulator, part no 1197311545, for this alternator costs more than $400, buying it doesn't make any sense, so I got one from Mobiletron for $30. It will be cheaper to buy proper facelift alternator if this one failed anyway. Proper one would be this 120A Bosch.

Sounds like battery is not fully charged. When you charged it, how many hours at what amp charging rate?
What is battery voltage with engine idling?

14 hours at 5amps on 80ah battery, even if not fully charged, I suppose it should be enough to start the car at least once, without any additional load, everything turned off. Battery voltage at idle is around 12.4-12.5, old, drained one was idling at 11.6v, triggering battery light periodically.

 

Sounds like battery is not fully charged. When you charged it, how many hours at what amp charging rate?
What is battery voltage with engine idling?

 

Maybe the wire that runs to the starter

 

It’s nothing wrong with the original alternator; it’s the bad connection from battery to the jumper post or the battery to the chassis that had caused your starting problem and the low battery charging voltage. When you measured only 12v at the battery at idle, I bet it was 14v at the jumper post to chassis.

 

Removed terminal from battery post, cleaned it with wire brush, put it back together - measured resistance is lower than 1 ohm.
Rechecked resistance between battery and alternator positive - less than 1 ohm, all set.
Started the car, with new voltage regulator voltages are at 14.4-14.5v instead of old 14.0, runs and purrs like new

Thank you markusmarkus and BaliDawg, I hope this will also help other guys in similar trouble!
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I've read the thread, but haven't understood what seems to have the been the problem. Was it as simple as cleaning the battery posts and terminals? If so, whenever I do this, I coat with vaseline.

 

I've read the thread, but haven't understood what seems to have the been the problem. Was it as simple as cleaning the battery posts and terminals? If so, whenever I do this, I coat with vaseline.
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Bad contact between positive post under the hood and cable going to starter because of oxidation, resistance was pretty high - 800 ohm, when I was jump starting it via positive post enough power got through to starter, but alternator couldn't charge the battery. Cabling between battery in trunk and post under the hood\between alternator and starter was fine. Brushes were nearing end of their lives, so I don't regret removing alternator and changing them, this improved voltage at idle by 0.5v

 

Bad contact between positive post under the hood and cable going to starter because of oxidation, resistance was pretty high - 800 ohm,

If this is true then there is no way it can be jump started at the fender post. You said there was 800 Ohms between the fender post and starter, but you also said jump start was OK at this post. Impossible!!

The root of the problem is the bad contact between the battery cable bolted to the jump post, period. The also explains why the normal alternator could not charge the battery (only 12v), and I bet it was measured around 14v at the post.

Every regulator will output the voltage slight different from the other, and so 0.5v different is within the spec; IOW, one might have 14v and the other might have 14.5v even though they are both brand new. That 0.5v has nothing to do with the new brushes.

 

I'd suggest checking the earth cable. There should be one if I remember correctly, connecting the engine case to the chassis and thusly grounding the whole engine. They tend to corrode and have contact resistance, which can choke the current flow down to a point where you might think the battery is flat.

 

A genuine Bosch voltage regulator from FCPEuro is $30. Here’s the link: BMW Voltage Regulator - Bosch 12317559183

 

A genuine Bosch voltage regulator from FCPEuro is $30. Here’s the link: BMW Voltage Regulator - Bosch 12317559183

As I said, it doesn't work with this alternator, mine alternator seems to come from pre facelift junkyard car, p\n of regulator is 1197311545, photo attached (looks completely different), link BMW Voltage Regulator 12311713491 - Bosch 1197311545 | eEuroparts.com® . If you have original facelift alternator on the car - sure thing, get 12317559183

 

There are times a resistance check is called for. Other times a voltage drop test is called for.
I have to believe that if a voltage drop test was performed, that there would have been a significant drop somewhere along the line.
The above clearly demonstrates the different outcomes of the two different tests.

While the voltage regulator solved his charging issue, the reason it wouldn't start was the inability to carry enough amperage (sometimes in excess of 200A) to the starter to get the job done.
The now working alternator is keeping the bank (battery) filled up.

 

It is outlined it the OP

Charged the battery using charger - nothing happens, bought new one (Exide AGM 80A\800CCA) - same thing - voltage drops to 11.9-12.0 when trying to crank, nothing happens besides one click.

There was voltage drop and high resistance, caused by oxidation, was the cause of drop.