What year is the motor? Do you have a Yamaha service manual for it?
I'd say its fuel related. Do you have a Racor filter installed? How old is the element? Do you notice if the fuel primer ball is collapsing when this is occuring? Can you pump the primer ball up firm with the motor OFF? If not then it could be your fuel pumps (either one or both...), bad diaphragms. If its a late model ProV with the larger underhood filter element that element should be yellow if its clean. Brown if its dirty.
-Mike