First and easiest thing is to check simple fuel related stuff, start with the filters, if they're more than a few months old they should be replaced anyway, make sure when changing fuel system components you drain everything into clear containers to examine water/contamination, I've been amazed a few times at what has come from a fuel water seperator.
It could be any number of things, but fuel system contamination is usually easy to diagnose, I typically drain a racor filter atleast once a week when a boat is constantly in use, doing routine checks like this always helps prevent bigger problems from ever starting.
The other things you can check are simple, harness connections which may be lose, any wires which might be coming in contact with heat/salt/water causing them to degrade. Especially ground wires or ignition/computer related wiring. Misfires are fuel or ignition related so something as simple as a severely corroded ground could be causing an issue. A thurough visual inspection of these type things is simple and should also be routine from time to time.
Also remember that anytime you have misfiring you should examine all your spark plugs, even when caused by other issues often the plugs take a real beating from being run with improper mixture. Realistically the goal is to do every simple check you can before calling in someone who will bill you to do the same simple things.
Working as a captain I've learned the best thing to do is do a comprehensive check of all common-sense causes, and if you cannot locate a problem, you will be prepared when you do have to call someone who bills $70/hr. Its much easier for a mechanic to get the job done efficiently when you have a list of checks and results to give him when he arrives, all these simple/small checks add up to big bucks. Instead of spending two hours thrashing away at filters etc. he will be able to start with ECU checks, fuel pressure checks etc.