If you hunt around like I did you may find a cheaper alternative master cylinder. I found that an Aprilia road bike (Brembo) one was the right size with holes in the right places for nearly half the price of the Beta one. £30 odd if I remember correctly
Maybe be the throttle cables are for the original throttles and not the modern type shown in the photo? Not an ideal solution, but you mention the throttle cables is too long. How about unwinding some of the outer cable to make the correct length?
I run the Beta Factory exhaust on mine I wonder if that makes a difference? I've never had to touch the carb on mine or use the hot start. Plug is a lovely brown colour too.
If the valves were rocking they could have been on the top of the lobes= 1 complete revolution out. If so no wonder it won't start as the valves are probably not opening
