Ok, new gas, soaked and cleaned carbs and new plugs. Idles fine but when I throw it into gear and add gas the motor chugs a little then chokes and shuts off. Both in forward and reverse. Does not run great in emergency either. Thoughts?
What does it mean when you say "does not run great in emergency either"? If all you did was soak the carbs and did not totally disassemble them, clean all the passages and jets then you didn't get the high speed jets clean.
Compression test should be the first thing performed when chasing a running fault. This will give you an overall picture of engine condition and often stops you from chasing your tail (so to speak).
When the fault happens, try pumping the bulb, could be bad fuel pressure. When the carbs were off, did you inspect the reed valves?
Did you install the new parts from the carb rebuild kit, including needle and seat? Did you carefully check the float level as per the workshop manual specifications. Are you sure the little 'o' ring seals are seated in the grooves correctly?
If you are sure that all of the above is o/k, time to look at electrical. Bad coils (and plug wires), plugs, CDI unit etc.
__________________
Watch this space......................
last 3cyl CDI I sold the man still has the 365 dollar part in his box as a spare.
as you go the electrical,and most likly wrong route,
you will need the service manual and a CD-77 multimeter or a DVM with a DVA attachment to check pulser coil output,stator output and CDI output.
there is just not much that fails on that motor. check your compression,at the same time test the spark.
do a forum search on a homemade spark tester.
go back,dissasemble or replace the fuel pump,remove all the carbs. carefully dissasemble and clean all jets and pasages.
while powerpack/switchbox and ign coil failures were very common on jonnyrude and merc stuff its just incredibly rare on yamaha stuff.
its also why we dont stock any CDI units or ign coils.
why would you wish to test the rectifier for a stalling issue?
yes they can both be bench tested but resistance tests are normally useless especially since Yamaha doesnt specify the meter imput impednce for testing. thats why we use output voltages. much more reliable.
that engines ign system is very reliable and easy to troubleshoot.
so test compression,test spark,fix the fuel system is how it normally goes.
one easy no cost thing to check (that I have seen 3 times now) is the timing advance, make sure it is moving freely when you advance the throttle, if it is stuck, then the Motor will die when in gear and throttle is advanced, now by all means follow Rodbolts tips, probably no more knowledgable Yamaha person in the known World, but I thought I would let you know what I have seen before, and cost nothing to check, as well as you do not need to pull anything to bits or throw a bag of parts at it to try.