Nice!
I recently did a HID conversion as well on the 900FE.
FWIW, I just used the OEM headlight assembly and replaced the H4 halogen with the HID bulb (+igniter & ballast). By using the OEM headlight assembly you also keep the reflector properties of headlight/bulb which works better for an HID system than a projector headlight/bulb, as yours seems to be. See:
http://www.geocities.com/edwyun/bbg1500.html
As for the wiring, if the HID's are both 35W, in theory and as long as your electrical system is in tip top shape, it shouldn't be too taxing on the bike's electricals for you to ignite them both. But I think the issue is that on the 900ss, when the high beam is on, the low beam is off. I guess you could splice into the wiring harness and run 2 sets of wires from the three-prong OEM headlight socket but I'd look into getting thicker wire to handle it if you do so (BTW, my three-prong OEM headlight socket has three wires - black, yellow, and white, and then there is another black blade socket and another yellow blade socket - is this what you're using for the second HID bulb?).
Also, even with 1 HID bulb, it's enough to annoy other drivers on the road. 2 HID bulbs and I'd be worried about truckers and cars running me off the road.