 RE: Yamaha F250 Help
You need to do some basic diagnostics. One of the first tricks is to see if the engine is running on all cylinders: pull one spark plug wire off at a time (alternatively you can disconnect the wire to a fuel injector). If the engine runs rougher without that spark plug wire connected - that cylinder is OK. If there is no change in RPM's when you remove a spark plug wire, then that cylinder isn't firing and something is wrong. If only one or two cylinders aren't firing, then you can rule out systems that are common to all the cylinders (like fuel pressure, computer sensors, etc.) The question now becomes "is the problem spark or fuel or compression"? It's easy to check for spark with a spark checker (mine can check up to four cylinders at a time). If the spark checker says you are getting juice to the plug, that's good, but doesn't mean the spark plug is firing, so put in new plugs to be sure. Still run bad? It's time to check the fuel side. Try swapping fuel injectors and see if the "dead" cylinder changes to another position - if so you found yoru problem.
If all cylinders behave the same on the "drop test" (as we call it) above, then it's probably the fuel system, though in some rare cases it's a computer sensor or something else. Best bet is check fuel pressure next. All four stroke motors have a port where you can hookup a fuel pressure gauge downstream of the electric high pressure fuel pump. If the fuel pressure is low, then the question is why? It could be the VST filter, could be the high pressure fuel pump, the low pressure fuel pump, the hi or low pressure fuel filters, a fuel check valve (there is one on the engine on Yamaha's), the fuel water separator, the anti-siphon valve, the fuel tank pickup tube, etc. Running the engine on a separate tank, hooking it up at various locations on the fuel system can help eliminate (or pinpoint) some possible problem areas.
Based on my experience, the following info may be helpful in pinpointing exactly where in the fuel system the problem lies. This info does NOT the gospel, but more often than not, it will lead you to the problem quicker than random guessing. If nothing else, it's a method for trying to make sense of the madness:
1. Engine surging, fluctuating RPM's, or sudden drops in RPM at higher throttle settings tend to be RESTRICTIONS in the fuel line UPSTREAM of the fuel vapor separator. What's happening is that the fuel vapor separator is running out of gas, when that happens, the high pressure pump (which is sucking gas OUT OF the fuel vapor separator) can’t get fuel and the fuel pressure drops quickly, albeit only for a fraction of a second. Since the low pressure pump is still pumping gas INTO the fuel vapor separator, as soon as a little more gas into the fuel vapor separator, the high pressure pump again has something to pump and can get the pressure up to where it should be – until the separator runs out of gas again.
2. Steady low power, constant rough running, or engine runs great but won’t reach normal max WOT RPM, tends to be caused by a restriction in fuel system DOWNSTREAM of the fuel vapor separator. Typically this is due to, presented roughly in order of the likelihood of the failure: a clogged high pressure filter (vst screen on a Yamaha, vst screen and/or high pressure fuel filter on a Honda), a failing high pressure fuel pump, clogged screens on the fuel injectors, or a faulty fuel rail pressure regulator valve. What's happening here is that fuel pressure is steady because the fuel vapor separator is not running out of fuel, however the pressure is low because the engine is taking more fuel out of the system than the high pressure pump can replenish once the engine reaches a certain RPM.
Unfortunately, these problems can be time consuming to diagnose in real life. A consistent, systematic approach in diagnosing the problem is extremely helpful – more so than a “shotgun” or “start replacing parts” approach.
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Specialty Marine 
26' Blackwatch - twin Honda BF225's | 
