[scuba scott]

I'm a new owner of this motor. The motor runs good at higher rpm 3500+. Top rpm 5400.

At low rpm I smell raw fuel and see fuel in water.

Where do I start to correct this?

[rodbolt]

check the 3 low pressure pumps, if one is leaking that is a symptom. if none are leaking then check the thermosensor and the enrichment pump and make sure the manual enrichment valve is off.
the 3.1L motors eat low pressure fuel pumps, they are about 35 dollars from yamaha.
replace the pumps as a service item about every 3 years.