It helps to remove the stud, I found that out when retro fitting the new cover. I removed the stud then put it back in once the alternator was situated. I do not fear messing with it now!
Anyone doing this I highly recommend getting the kit a few pages back with the alignment tools. I marked my brackets before we pulled it off the donor vehicle, and it was still way off.
I came up with the weatherstripping on the bar to keep the flag flapping sound down on my Trek top. I was going to replace the foam with some 5/8 heater hose.