With all due respect for my fellow members here...
Looking for a leak...if you have a leak before the lift pump it will be hard to find since it will always be under suction. You just have to go connection by connection and do your best. You could temporarily change our the fuel line leading into the lift pump with clear tubing provided you can find some with thick enough walls so it doesn't collapse. The clear line would show you if you have an air leak before the lift pump. You should see no bubbles with the motor running.
If the leak is between the lift pump and the high pressure pump you should be able to see wetness or dripping fuel.
If the leak were after the high pressure pump you would be running on less than all cylinders, and running rough so I don't think that's the case.
With the hours on the motor you have it's very unlikely to be a bad injector. You can remove them and send them off to be rebuilt, but I think you are barking up the wrong tree.
If you injector pump is so bad that it's leaking back I doubt your motor would run at all. Normally injector pumps do not leak back what so ever. It's also very unlikely the problem at the low hours you have.
You should be able to crack the bleed screw a little on top the secondary filter with the motor running and fuel should squirt out. If not you may have a weak lift pump. Again, this is unlikely since it's a new motor.
If you don't have the Yanmar Parts Manual and Service Manual you should buy them.
You might find taking a class useful. I've worked around diesels for many years, but I learned a lot by taking a level 1 and 2 class on marine diesels. I learned a ton and have put what I learned to good use on my boat.