New Airhead wiring harnesses can get terribly expensive. There's a front harness and a rear harness and probably a tandem hitch horse harness in there, too.
Buying old ones off eBay gets you, well, an old harness that may have hidden faults much like the one you already have.
Making up your own, brand new, Airhead harness is a doable project. Reusing some of the BMW connector blocks can be done by replacing the interior contacts. They can be removed quite easily.
My concern, and likely yours too, is the multi-color wire with those lovely tracer colors. Here's a source for the needed wire. Sold in a minimum 10-foot length, you avoid having miles of left overs.
Quality electrical connectors and terminals are as close as your local hardware store. Klein crimpers are a good investment.
Check out Rhode Island Wiring Service, Inc. for your wiring needs. Your existing harness is your pattern. Take a couple hundred digital photos before stripping the bike. Replacement of the new harness will be less stressful.
Good luck. Have fun. Post finished pics!
http://www.riwire.com/Monte