Puffin - 2 things: have you test fit your battery and side cover (or is the location different from stock?) with the Reg/Rec mounted sideways? Its a good location, I just don't seem to recall enough room there with the stock battery box in place.
And I can't tell from the coil pictures, just making sure your 2/3 coil has the BLK/WHT wire to the top screw as you have on 1/4. And I only ask because I can't see, even though I suspect you have it right... But I always ask to make sure on things like that.