If you believe it to be the top oil seal remove the flywheel to see how far out the seal has moved. It might be possible to tap it back in place. Then fabricate a retainer to hold it there.
Did the pump rebuilder pressure test the pump? If the pump is not outputting rated pressure while it is being supplied with the gasoline it requires, what else could it be? Pressure regulator being part of the pump of course.
Who rebuilt the pump?
This is from a 2007 Tohatsu owner's manual for a 9.9 four stroke. There has to be wires from either the lanyard kill switch of the push to stop switch at the end of the tiller handle.
The main engine harness has ten pin connectors at each end. One of those pins in the connector being used for Yamaha motors that have have a choke system for fuel enrichment.
Your new motor, having fuel injection, does not use the wire for the choke.
Pushing your key in when starting the...
With the pump running and the motor off (say at key on but prior to start) the pump pressure will be at its highest. Maybe 40 psi or a bit higher.
Start and run the motor at idle RPM and the fuel pressure should drop. Maybe to around 36 psi or so.
Increase the RPM and the fuel pressure will...