I'm running 3" exhaust and I just have it tucked as close to the differential as Six_Shooter stated above. In his second to last picture if you view the differential there, a little knuckle or tab or whatever you want to call it extends off the diff. Grind it off. It's not needed. Let's to tuck it up just a tad bit more and you don't have an annoying banging noise if your exhaust moves a little bit. Also if your exhaust rubs it too long there will be a hole there. Notice the marks from it in Six_Shooter's pictures.
Another thing that allowed me to tuck my exhaust up really high was the fact that I've got an RT diff mount and I took the factory diff mount that holds the control arms up, and section the middle out and boxed in the ends that hold the control arm up, that way they are still strong and do their job, but the diff mount is out of the way. Some will say I've sacrificed chassis strength. In my opinion the RT mount is adding any support I may have removed from the chassis right above, most likely more than I removed seeing as how its made of thicker steel. As far as clearance this gave me, when it comes down to it it only gave me more clearance in the transmission tunnel because I've got the exhaust higher in there. Really though that is where it was needed because that is where speed bumps and other things are most likely to hit the exhaust. Seeing as how the wheels are right in line with the spot that you're having troubles with, it will be going up as the wheels do on speed bumps.
Beyond that I would agree in saying either oval or square/flat tubing would be the only other way to get around that, short of cutting holes in the floor and running the exhaust inside the car and over that, which just sounds insane unless you're building a race car.