I thought they are designed to keep up with the needs of a vehicle and motor to keep the battery from being drained while running not charge it from dead.
if it is dead there is a good chance the battery is bad to start out with.
heck even in automotive they say not to jump off a dead battery...
best thing to do is keep the batteries charged up
do not expect a dead battery to be charged up from the outboard itself
it will do its best to try ,but that can over task it
Vapor Separator Tank
that is where the fuel pressure pump that feeds the injector rail resides.
you should have a lift pump the takes the fuel into the VST.
sounds like you need to take it into the shop since it is under warranty
your original post did not say the primer bulb was hard, it said it was soft.
It seems like it runs out of fuel even with a full tank (portable tank) the primer bulb goes soft
once you hook the fuel pump hose back onto the pump do you pump the primer bulb to fil the VST with fuel before...
did you try pumping the primer bulb to push more fuel into the system?
is this a fuel injected motor?
you said you have to remove the output hose from the fuel pump,
is it really the fuel pump or was it the primer bulb?
You should be looking for what the 3 beeps are also
should be a bushing, clean up the drive shaft and put some waterproof grease on the shaft to keep the rust away and the bushing to lube it.
I bet your owners manual calls for lube from time to time.
but I do not know how that would cause a knocking noise
verifying the rail pressure before cleaning the injectors, would have been a better idea, but it sounds like you have it running a lot better now.
and it never hurts to verify the rail pressure is and staying in spec
I never torque those, just tighten up where it feels good to me.
but I was an automotive tech in an earlier life.
I have never seen a Yanaha manual that covered all those HP motors before, so I think it is an aftermarket manual you have
if there are signs of the plastic housing melting, you should replace that.
also did you make sure the damper parts in the housing were in good shape and in place.
(Where water tube heading up to power head go into)