same weird gig here on a 98 challenger, but only does it on the Starboard engine...
new engines, all carbs rebuilt with Mikuni kits and all in spec with all new needles and seats. and replaced the plugs after engine break in. Also 2 new accel pump diaphrams installed.
I thought it was just a learning curve. being used to EFI ski`s.
if I shut the boat down, it will refire right up. if the boat sits for more than 10 minutes or so, the starboard engine will take a bit of intermittent cranking to fire over. What I learned> when I shut the boat off for more than 10 minutes, I have to push the throttle lever 2x no choke and it will turn over, no stumble, good idle right away and it will continue to run good...
just weird. really don`t know other than maybe fuel evaporating in the hot engine.
14 year old seadoo fuel pumps (2) were replaced with 2 HV Mikuni dual outlet pumps and each carb has it`s own fuel supply.
So I`m still learning and watching on what`s going on...
what I did notice before the repowering the boat was that the throttle cables were improperly adjusted and the starboard cable did not fully return, resulting in a hard start. Both Mag carb throttle shafts were hanging, and both were disassembled and fixed.