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...
I've got the UPR box but haven't attempted installation yet. I was wondering if the inside quarter panel will interfer with the box at all. Right now I have the interior stripped out of the car due to restoration and thought I would ask before installing it this weekend.
That is partially why mine sits back so far and thus causes problems with the hatch cover... If you try to move it forwards, it hits on the inner fenderwell bend in the panel causing you to then have to move it towards the center of the hatch... The only problem with that is that you then have one of your attachment bolts running into the spare tire well rather than immediately into the floor pan... I think you can solve this by turning the box length-ways, but my box had the cable cut-outs where this wouldn't work for me...