I was lucky with my last boat and never had to do much with the engine. That being said, your boat should be TBI, mine was. I could walk you through some tests with fuel injectors, but I'm not sure how to test the TBI system. If you end up brining it home to troubleshoot, people are always here to help. Mike and some others are full of knowledge.
Mike, on my 2000 350 mercruiser, I had a regular spin on fuel filter. Same as my 2003 I have now. Maybe they were including something else in that price. Engine serial number would help clarify some things.