Welcome Aboard !

Yes, removing one of the battery leads is a must when the front engine cover comes off.

• Your actions would not normally cause the whole system to "go dark". There is no "main fuse" on a BMW harness, but an owner might have added one back near the battery. You did not say this, BUT if your whole system went down after the "spark", then you might want to cast around and look for a fried owner-installed fuse. These are usually placed back near the battery.

• There are 2 ways to test the alternator output at home. One is by removing the rectifier and test the components on the bench, which requires going back in where you just finished working. (Happy thought.) The other is to test the health of the entire charging system while running, which requires removing the starter motor cover. Neither is a 5 minute job. (If you're really good with your hands then you might do that same test at the battery, but..)

A simplistic explanation
I like the second option, but the /7 only has electric start, which means you need to connect meters in such a way as to still have use of the starter motor. You can do that at the RED wire at the starter motor, or you can juggle cabling (and sparks) back at the battery. You'll need a voltmeter in "parallel" across the battery terminals, and you'll need a DC ammeter (of at least 10A) in series with the battery after the engine is started.

With the engine running at road speeds (~3000 RPM) you'll want to see more than 14V at the battery, and a positive current reading constantly on the ammeter, headlamp ON or OFF, heated grips ON or OFF, brake lamp ON or OFF. With a "blown" rectifier I'd expect good voltage, but not enough current to keep the ammeter in positive territory when the load is greatest. You see the 3-phase alternator uses a rectifier with 6 diodes. Loss of 1 diode would cut the system output by 1/3. Loss of 2 diodes might cut it by 2/3. So if the original output was 12A, the next step down is 8A, followed by 4A. At some point (with a blown rectifier) the electrical loads might rob enough power to keep the battery from charging... and the battery MUST always be receiving a "positive" charge (as opposed to a "discharge"). (The horn and blinkers are not a valid electrical load for this test.)

If you do not understand the above then you need to buy some books, especially the "Classic Boxer Charging" by Rick Jones.

And don't forget to blow air on the engine while you do all this.

Hope this helps.

Thanks for all the info. I'm wondering if I should connect the ammeter in series and then start the bike, or if I need to start it then pull a cable to connect the ammeter. Would it be best to connect by removing the neg cable and running it in series there?

I'm wondering if I should connect the ammeter in series and then start the bike, or if I need to start it then pull a cable to connect the ammeter.

If you do that, then your DC ammeter has to read high enough to allow the starter current to pass, or you'll smoke your meter. But a meter that reads that high probably won't indicate something as small as 1A. And I think if you get the bike running and disconnect the cable, the ignition will die. So you probably need to make the ammeter connection, then hold the battery lead against the battery terminal manually just long enough for starting. That's why I said "Lots of sparks". 😛

Would it be best to connect by removing the neg cable and running it in series there?

The energy going through the Positive terminal of the battery is EXACTLY equal to the energy running through the Negative terminal. Therefore it makes no difference which terminal you choose.