Yes it will fit, you'll need the offset intake, you'll probably need to remove a tiny bit of material from the crankcase in the groove between the front mount a bit. Maybe not if you are lucky and just have a nice tight fit. You can always leave the head off for putting it in.
Jackshaft possible but requires modifying the bracket. Left side drive will work, remove disk brake and rotor and hijack the rotor mount. It should line up well but you'll probably need a spacer between the sprocket and hub. Alignment is just removing a washer to the other side really, or mix and match spacers and thin axle locking nuts.
Large frame is better, one thing I like about these taller bikes is you can see a lot around and ahead of you compared to the shorter sitting ones, I also have a bad habit of standing on the bike so that might affect my judgement in that realm though...
Larger wheels roll over things and lumps better, it's ridiculously easy to hit a bad spot and puncture a tire on the 26 and lower wheels with small diameter tubes. After switching from a regular 26in mountain bike wheel to a wider and larger diameter wheel the tire issues disappeared almost entirely, only running over something sharp would break it, curbs, lumpy park trail crap, bricks.. they just don't pop as easily on big tires, just big tires increase your chances of running over something that will puncture it lol..
The muffler will be a b**ch, you'll have to get creative and do some bending or some denting (in my case both, always.)
Definitely worth the initial investment, you'll at least be starting with something that can actually handle an engine being jammed into it. They make good centerpull brakes that can be used on the rim. Keep front disk but definitely upgrade it.