Here's a 4T with the rear body work removed. That's just a U shaped piece of sheet steel with a weld nut on one side. I'll draw up a picture of what the bottom bracket would look like, but for now imagine two U's welded perpendicular to each other.
Exhaust might hit, but like someone suggested, a custom exhaust with a really long header and the box/expansion chamber where the spare is would give maximum ground clearence. A longer header might give your more low end grunt like on a 4T, different reasons but both are because of pressure waves in the exhaust gas. A larger volume exhaust on a 2T delays the reflection of the postive pressure wave, boosting low rpm power. This effect was and still is used on highend 2T bikes to tune the exhaust to the current RPM range by opening and closing a servo controlled valve into a large chamber in the head or exhaust. Could rig up a small tool box, extra tank, or battery compartment to run big spots in the rest of the space.
Regarding full compression of the shock and the exhaust hitting ground, you can control suspension travel with spacers and stops/buffers so it doesn't happen. Plus a very stiff shock, which will mean 'riding the pegs' so you don't hurt yourself, think broken back or neck.
I would suggest using a 4T frame as a base, it would give you lots of room and is supposedly stronger and stiffer than the monocoque.
I'm now imagining a rally/endurance bike based on the P. Rear rack with spare tire, supplies, gas, tools and spare parts in the glove, fuel tank atop the center tube, two floodlights mounted on the legshield, front rack with bivy/sleeping bag, long suspension travel in the rear to make up for the limited travel in the front. Exhaust and battery in the spare side cowl. I'd probably base it on the 4T, keeping the 4T engine but with extensive modification like Polini 165 kit, porting based on substansive building up of material around the ports, possibly adapting a 3 or 4 valve head, maybe even liquid cooled or just an oil cooler. Actaully maybe keep it air cooled for simplicity and reliability, less to go wrong. 4T might be a little more reliable in off country conditions and definitely more fuel efficient. Actualy with the 4T you could keep the spare as is and run a straight pipe with a small silencer/glass pack or even nothing. Skid plates and protectors all around. Fuck, time to find a totaled but useable 4T.
I could say I should build a trail/endurance bike based off the Cub but Bob Uhl already beat me to it by over half a century. To give you some motivation, back in the 60's, an American executive of Honda Motorsports America noticed one dealer in northern Idaho was selling more Cubs per month, basically an urban commuter bike, than all 4 dealers in LA combined. So he went to the dealership to see why. The owner, Bob Uhl, was fitting a second, higher tooth rear sprocket, a cheater sprocket, to lower the gear ratio and increase torque, knobby tires and other offroad mods, to create, with the Cub's low weight and auto clutch, a easy to handle and operate trailbike, basically the first dirtbike, and selling them to hunters, farmers, ranchers, and people just looking to ride trails and have fun. For comparison, trail bikes of the time were based on high powered, heavy roadbikes and took considerable skill and strength. The executive thought 'hell, Honda should build this.' Thus the Trail Cub was born and possibly the modern offroad bike and its sports.
