Check the running voltage at the B+ terminal ( the large 10mm one on the side of the board) the voltage should be the same as at the positive terminal on the battery. If not you could have a burned wire that runs from the B+ terminal to the positive stud on the starter. I fought with intermittent charging problem for a whole summer, until when replacing a timing chain I found the wire to be very stiff and hard feeling. Cut off the heat shrink tubing, the wire insulation under the tubing was burned and stripped the wire insulation I found the wire to be corroded and burned from excess heat (resistance). Replaced the wire I have had no more charging problems.
A quick way to check the diode board with a digital VOM is to:
1. Place the VOM on the AC voltage scale
2. With the engine running, measure the voltage between the positive and negative terminals on the battery.
3. The AC voltage should be near "0" zero. If you read any more then a couple of tenths of volt indicate that you have a defective diode on the board.
I learned this test from Matt Parkhouse's keep them flying article in the January 08 BMWMOA magazine.
Rich running on one cylinder, check that the choke is pulling completely off, try pushing it closed with your finger. The cable may be out of adjustment. Also check that the slide needle in in the same slot for both carburetors and that the diaphragm is positioned in it's proper position. You would be surprised how well these engines run with the carbs messed up, and how much better they run set up correctly.