Given how long it had been sitting, check the jets and piston valve of the carbs. Might as well clean all of them.
If carbs are good, need to look at sparj.
Cylinders 1 and 2 run off different coils so the coils are not the issue. But 1 and 2 could have bad caps, or bad wires, or poor...
You don't have much clearance, I'm guessing it would have to be much stiffer. If it is really bad, you could go with a slightly taller rear suspension but keep in mind you are altering the bike's geometry and both riders will then be leaning a bit forward. Unless you find a slightly taller...
I'm not experienced in hoops, but the flare up at the end of the seat is usually right where the rider's ass ends. If you bend it up, your passenger is going to be leaning forward onto you instead of being upright.
check your spark plugs. If they are black, you need a lower main jet. If they are much cleaner, with only a small amount of grey, you need a larger main jet.