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)
If a bolt was still holding it ,I do not think the lower unit would move 1 " apart like he mentioned
I still think he has to disconnect the shift shaft
I believe that old of a motor would be a push pull shift shaft not a splined shaft that twists.
so you would need to loosen a lock nut and unscrew the barrel nut on the shift shaft to separate it
I am sure your service manual for that motor would help you understand what to do and how to do it.
You might even find help on U tube
the owner's manual might even tell you how often to do things
I would check to see if you find water in the filter or carb bowls.
sometime if a small amount of water gets into a carb jet, pulling the choke may help suck it thru to let gas flow again
This is only a thought I had
to me I do not see how a motor that was running too rich could be helped by...