With my insulated floor I have exactly 6 feet in the middle of the bus. I'm 6'5"......
Buses have an extraordinary amount of ground clearance really. The parts that hang low are the axles and stepwell. A person could modify the stepwell easy enough though it's going to make getting in and out of the bus that much harder. You could gain a little room under the axles by running the tallest tire you can fit without hitting fenders. The tranny pan and oil pan could just get a healthy skidplate to protect them. As far as lifting a bus....well....it's quite possible and would be relatively easy to do, but I would rather not offer advice on that because I don't think it's a good idea for any purpose other than exhibition.
Just learn what the low point are on the vehicle and keep them away from the high points on the terrain. Drive with a tire on that big rock, not straddling it. Just how far offroad are you planning on taking this thing? My bus has been down many a logging road and skidder trail without issue. I also don't go places that are going to get me a $2500 towing bill (Jason