1999 yamaha 100 4s running rough intermitant.

Thought we sorted rough mid-rpm(#2700) with Sea Foam but returned last trip with rough running at #2200 but even after it goes away a hour? later and runs 'normal' it still has a vibration at cruise rpm (#4500-5000). Thinking it's a fuel problem (air leak?) so replacing fuel bulb, hoses and rebuilding fuel-lift pumps? It's got #3200 hrs. of hard saltwater service so starting to think it's a warnout part???? It's got me really scratching my head and appreciate any input I can get. Quite a change in our 'bulletproof' feelings considering we've had it #125 miles offshore of San Francisco. Thanks Bob