Only did this once but no problems as you describe. Is it possible the inner is tweaked/twisted from over/inequal torquing?

 

Thanks guys, I was just looking to vent.
This project was quite the PITA between the ignition switch and now the outer fairing won't line up.
I did cover the spots and took a boatload of pictures. Everything looks correct but it just won't sit back in right.
When it's warmer this weekend I'll tackle it again.

Thanks,
Charlie

 

Had the same problem when I put mine back on. I had one of the main wir eharnesses on the wrong side of the upright bracket. All of the wires go behind the brackets. Then it went right on.