did you follow the link and sync procedure in your service manual after you put the carbs back on?
all 3 carbs throttle plates need to completely closed and tied together so all are contributing to the idle the same.
(not just set at idle position)
also the timing is part of the procedure
you have not reported what the timing is doing with the new CDI box installed.
at start up my C40TLRX shows around 5 BTDC and idles high.
once warmed up it drops back to 7 ATDC.
what does yours show?
also post up a pic of your new CDI box hooked up.
I am not following the problem with the...
there is a chance you have a leak between the pump and fuel tank allowing air to be sucked in,.
But then the pump runs off of the #3 crankcase so it just pulses ,so does not run a steady stream.
rereading your other post, if pumping the primer bulb helps then look for an air leak between the...
Only T50 I found listed was on a 15'7" toon
I would not be expecting much on a 20'
https://yamahaoutboards.com/outboards/jet-drive-high-thrust/high-thrust/f50-(high-thrust)/pb_god_mighty-g-cruise_t50lb_8-7-2022_pnt
a t50 pushing a 20 ft pontoon?
not much motor .
have you looked at what other people are pushing a boat like yours with?
also what prop they used?
look at yamaha performance bulitens online to see if they list a T50 for a toon like yours ,
and if so what prop that used.
was that a Yamaha service manual or an aftermarket one?
Boscoe said the Yamaha service manual and owner's manual
by the way you mentioned copper ring on some plugs,
copper and aluminum do not get along well touching each other
simple to start draining the tank slowly and see when it refills
but I would think your service manual for your motor would tell you about how far it would move to set the switch
sounds like a lean sneeze.
and pump is not doing its job if pumping the primer bulb helps.
check to make sure pump is still good,
and the idle jets/passages are feeding the fuel needed for each cylinder
idle timing is After TDC, ( retarded timing)
WOT timing is Before TDC.(advanced timing)
guessing at what the timing is actually doing by looking at the none functional wiper does not help at all
if timing is not close to correct with the wiper pointed at the marks, then I would say it needs replacing.
what does the timing light show the timing at when wiper set to where the motor will run?