OK, let me get this straight: you had the Switchblade system before you purchased the lowers. When you installed the lowers last fall, you didn't turn them around (without the lowers the thick ends of the spools are inboard). The deflector didn't fit, but the 2up did. NC recently told you to turn the spools around (thin side inboard). Now, the deflector goes on, but both shields are rattling?
Here's a couple of ideas:
1. Your 2up has been sitting on the bike with the spools reversed for the last 4-5 months. This could deform the windshield's hardware, spreading it out, so that now, when you reverse the spools, there's too much play. The deflector now fit's loosely because when you put it together it was on the formerly wider Switchblade mounts. This is a bad scenario because it might mean your 2up is a bit messed up. I would imagine when your bike has been sitting in the sun a bit, this summer, it'll eventually mold back to the correct size for the reversed spools. The deflector hardware can be loosened up, installed on the bike, and should fit snugly once you re-tighten the hardware.
2. (The simpler, preferable scenario) When you installed the lowers, you left the 2-up on the bike, and adjusted the mounts so that it would conform to the 2up. Now, when you got around to reversing the spools, you loosened, but did not reposition the mounts. If so, the mounts would not be set out wide enough. Did you check to see that the mounts are parallel to eachother and not cocked a little forward or back?
The best thing to do would be treating it like you're going from scratch. Get the mounts on the bike loosely. Adjust them so that they are squared up and down the fork. Install lowers. Put spools on bike (thin side inboard) Tighten by hand. Put on the shield. Adjust mounts, if necessary. Torque to spec. (Go out and ride for a bit, then come back and readjust/retighten as necessary.)