I don't have time to go indepth, but I will, have no fear. I also don't know how much you know about bikes, so if it feels like I'm repeating a bunch of shit you already know, ignore me. But real quickly --
A V6 engine has six cylinders, not twelve.
820 pounds. In a 100-inch-long package. So you know, most bikes vary between 50-70 inches in wheelbase; you can safely add twenty inches to that for total length. For example,
Harley's VRSC is about as long as your bike, and it seats a pretty big V-twin engine. It alone weighs nearly 700 pounds, and it carries four fewer cylinders than your smallest bike.
This isn't to discourage you. Just keep this stuff in mind. An engine with as many cylinders as you're speaking about, with the speeds you want to achieve, is pretty fucking amazing. You should consider how this engine would be set up -- think maximum lean angle, balance, cooling, so on. What you have created is a bike that current technology simply could not create. The cylinder size on a V12 machine would be incredibly small; otherwise the engine alone could be 50 inches long. Cylinders that small are prone to breaking unless the metallurgy is something like tungsten alloy.
Inline engines, like those on sportbikes, are used for a reason. Their balance and road-handling is generally superior to a V-shaped engine, due to how V-engines work within motorcycle frames. The maximum size of an inline engine, however, is six cylinders (Honda and Kawasaki both made sixes, though only Honda perfected the technology). With the Lorath's technical expertiese, their physicists and engineers would realize this.
Don't restrict yourself in terms of shape, but share your vision with us as far as appearance. Is this a cruiser? Sportbike? Cafe racer? Dirt bike? A mash of them all? Shape is important in this case because it determines engine placement, handling, and speed. 220 mph is unreachable for any stock bike on the market today; extreme modifications, weight shaving and one
hell of an engine would be needed to reach that speed safely. For the record, a V-shaped engine that extends beyond the engine frame (sticks out the sides) would kill your aerodynamics, and you'll run into problems with shit hitting it. Consider using some fairings to shape the wind around it.
Stonethread fiber can resist direct strikes. That's good. But how quickly does it shred and break apart? Think abrasion resistence; carbon fiber is very light and can resist abrasion, for example. Is stonethread fiber like this? If so, excellent.
On the flywheel -- if you've got six cylinders, you don't need that flywheel. Your engine should be producing power through the alternator -- assloads of power, I dare say.
Okay, I should go to work now. You know Yosef will want one of these.