If at all possible I would install the bolt and nut as intended by the manufacturer. These things are set up that way for a reason. I agree with CSNOW, if you must install upside down I would probably drill hole and use wire tie or cotter pin to ensure the nut won't back off and bolt fall down.

I found little if any clearance with bushings in, but after prying off bottom bushing and pushing up top bushing I had plenty of wigle room to get bolt out and new in.

Good luck,
Joel