Re: misses at wot
My C40 had a WOT miss and it turned out to be running too rich because a previous owner apparently drilled out the main jets( maybe trying to make a 50 out of it) after replacing with new ones it runs fine. A leaking fuel pump will put too much fuel into one cylinder also.
Not saying that is your problem, but you need to be sure it has good compression and spark on all cylinders and that the spark is not dropping on a cylinder or two before looking at the fuel.
An inductive timing light or tach hooked to the different plug wires can help see problems on the individual cylinders. And the light will show that the timing is correct or not
A Yamaha service manual and the proper testing equipment helps the most.