Riding an unreliable bike is not fun and dangerous.
It is going to take some patience to fix all these problems.
The diaphragm may be able to seal the vacuum if you can seat it carefully.
The cable is a safety must.
The valves must seal because the base of the good functioning is a constant level of fuel inside the bowls.
Unfortunately, you need to re-clean all the little passages, including the ones for the mix screws.
Here is how:
http://faq.ninja250.org/wiki/Intake