I installed a Gpz1100 engine into a GPz750 frame after powdercoating the frame and gettingit all back together I found out the chain hit the frame at the lower rear cross member. I did not take that into account when I mocked it all up. I tried several solutions before arriving at one that worked. I used a sprocket to hold the chain off the frame, to bulky, I used a chain roller, too noisy. I finally just used an old chain slder I had. I cut the slider up and layed on top of the effected area. I then drilled a small hole through the bottom of the tranny cover and bolted the slider directly under the chain. Has been working great for two years now.
I would say the more clearance you can get the better. As the chain stretches it will hang down and unless you watch really close it will eventualy start hitting the frame. Had I to do it all over again I would have cut out the crossmember and moved it further down. I really don't like "smashing" any structual member.