Tom
If you haven't already figured out your problem, I have something for you to look at. I was riding around a few weeks ago and my bike (98 B6 with 1127 engine) started cutting out as if someone just tapped the kill button for a moment, and it was very sporatic. It took a while but I found out that there is a wire attached to the main wire from the negative terminal on the battery that has a small connector on it that plugs into the main harness, this connector was loose, and when I would hit a bump just right or something else, it would break connection and drop spark. I repaired this connection and that fixed the problem.
Later
Josh