I agree on everything except that 1996 engine as OP describes has the "system check" alarms with indicator lights. The overheat alarm lights over heat, the fuel restriction alarm lights the check engine light (as indicated in title). So, the overheat and fuel restriction alarms aren't the same w/ system check. Pre-system check alarms were horn only and what Bob wrote is right on for them.
First advice, get yourself a factory service manual or at least an owner's manual for that engine. Understanding warning signals and lights is basic owner information which is included in those manuals. There's also basic maintenance info. I found an owner's manual for my older Johnson engine on ebay, but are also available through other sources. It is handy to have and would have saved you a lot of wasted effort and money working on things that don't affect this warning signal you're getting.
Here's a helpful article too:
http://continuouswave.com/whaler/reference/VRO.html
As others have said, that particular alarm indicates a fuel restriction which not only has nothing to do with the VRO/OMS pump, it would also have to be corrected regardless of whether you changed the pump or discontinued the oil mixing system. It's a common claim of failure on the part of the VRO/OMS by people who don't understand it and an erroneus reason people use to discontinue automatic oil mixing.
Some common causes are restricted air vents in fuel tanks (can get plugged w/ critters nests), clogged or poorly installed fuel or water separating filters (which I strongly recommend if you don't have one!), faulty anti-siphon valves, fouled fuel pick ups in tank.
All that stuff is easy to check and correct.
Is this a new problem? If so, has anything changed?
