I used to work with a dude that wore His hat cocked way over to one side. Looked weird. Strangest thing I ever saw.
Then one day, someone pointed out the obvious - the hat was level and straight - it was the dude that was crooked! Physically and mentally!
Oh well, good luck with the alignment thing...

 

no, the top clamp would still be covered, just as it is now. the cover would still fit over it.

 

I can sorta see a slight twist to the right of your bars compared to the top tree. They ALL do that....seriously. Not a dealers line they do twist on the rubber bushings (the risers that is) and even picking up the bike and setting it back on the side stand puts a twisting torque on the bars and risers in the right hand direction. Harleys are heavy bikes and the bars move due to the stock rubber bushings. Not a big deal just something we live with. Correct it if you choose but it will twist again in short time. It was really noticeable on my softail with 6in night train risers and drag bars. I fixed it a few times but it always came back. No big deal. I'd rather ride than wrench.