Yanmar 2GMF looses RPM after a few hours of motoring.

[healeyman]

Check the primary fule filter. this was my problem... it often gets overlooked.

 

[RichH]

All of the other suggestions are reasonable, check for high vacuum in the ...

tank .. blocked vent
fuel lines ... 'bridged/clogged' with dirt/debris
lift pump ... loss of suction due to 'developing' rupture in the diaphragm ...

just temporarily put a tee with a vacuum gage on varying places along the fuel delivery line ... and monitor the gage readings referenced to a constant/reference rpm with the engine under load.

My suggestion:
Check the operating temperature of the packing nut / shaft log. Especially if you have 'flax' of 'flax impregnated with PTFE, etc.' and insufficient 'drips' to cool the packing, the friction can easily generate heat which can further 'close down' the flax to shaft clearance ... and the shaft will increasingly be retarded from turning as the temperature rises.
Simply, feel the shaft log before traveling, then feel the log at intervals during running, and especially when the 'apparent lugging of the engine' occurs .... if HOT, that it !!! and the Rx is to readjust the packing 'gland' to improve the 'drips per minute' or reinstall/replace the flax packing with GFO (braided teflon), etc.

 

[Steve Dion]

Engine condition:The engine has always emitted a sooty black exhaust that often coats our transom but has done so for 5 seasons. Engine temp hovers appropriately at 150-160 degrees once warmed up. Could the fuel pump be to blame?

Do you know your prop specs? If you have been emitting black smoke it sounds like a possible issue with your prop. I don't know how long you have owned the boat, but prop issues also cause this.

I would check out your fuel lines and filter for any possible issues too.