Tony:
Not sure what you mean by "clearance" issues unless you are talking about the hatch cover... Yes... I had a problem with it, but have a roll bar in any way so I can't use the cover... If you push the box forward somewhat you can still use the cover, but I wanted mine towards the back for weight...
I'm taking mine out now to go with the Summit polished box if you are looking for one... It is a Taylor polished aluminum box and I'll sell for $40 plus shipping...
You can see pics of my setup using the links below...