Hey, DucSoup! I do hope we can help you get your Paso running well again. Sounds like you've had a bad time - that's terrible about your bike sitting in that shop for so long. When you get your bike going again, go and park in front of the shop, leave it idling, go in, walk around, say in a loud voice 'Bad vibes in here!' (or something similar) walk out, and ride away.
Your electrics certainly look different to mine. I have Kokusan. I recently installed the relay mods designed by Gerhard and Jon Slocum to cure difficult starting, and my bike is running beautifully again. The installation was not difficult for me to do on the Kokusan system, even though I'm not good with electrics.
I think all alternator covers have only one pickup lead coming out, but there are two wires inside, coming from two pickups.
From what I have read, the Kokusan system is better than Digiplex. You may have to convert, and install the Gerhard/Slocum mods. If you spend some time on the web, you should be able to find the required information and sources. I'll let you know if I see anything.