Like most , I am assuming that besides the fuel filter/separator on your motor that you also have a separate racor type large combined fuel filter and water separator unit and because you have an outboard board, the separator is not the all metal type (fire prevention) for onboard motors designed for placment in the onboard motor compartment.
Yours should have a clear lower plastic lower section that will allow you to see how much water is in the separator. Get down and have a look and bleed off any water from the separator into a container. If there is none that may indicate the problem is elsewhere. This is basis boat maintenance and should be checked frequently and bled off as necessary. If it was full of water that may be the problem. If you have not done it recently I would buy and change out fuel filter, filter elements. This should be done as part of maintenance - some say once a year.
If there was water in your separator and possibly even if not I would check for the level of water in the fuel tank. Water in the fuel tank is more likely to occur in metal (aluminum tanks like mine than non metal tank because of condensation forming on the sides of the metal), especially if you don’t keep the tank full or near full during winter storage or periods of non use but can form in the plastic type tanks also. We always keep our tank filled up as much as possible and top up even if it was almost full to control condensation, provide the max fuel safety reserve for a unexpected turn of events out on the water, and use the fuel as ballast as my boat is poded, with the onboard heavy motor gone and some added air floatation in the pod. The long fuel tank is 80 gal of added weight low right on the keel line which provides a little added stability to my boat in heavy seas but decreases fuel economy a very small amount – more than a fair trade off. A full tank also help the fuel tank baffles control sloshing in the tank to prevent water and fuel in the tank from emulsifying or at least keep it out of the fuel tank pickup tube which is usually up a little bit from the bottom of the tank where it picks up less water and crap that will clog up you fuel filters and water separator.
On my boat I would remove the small hatch covering access to the main fuel tank pick ups or even the large hatch (screwed down floor board used to access and replace the entire tank) after ensuring the angle of the boat is good on the trailer. You want it as flat as possible for testing and to keep the gas in the tank when you open the top of the tank. Make sure the current fuel level is low enough, say only about 60% full to keep the fuel in the tank when you open the tank or you will have another big problem on your hands.
A complete inspection of your tank and all fittings and fuel line clamps etc. and replacement as necessary, is also part of basic periodic boat maintenance. Fuel lines are cheap; swap them out as necessary but buy the expensive high end stainless marine hose clamps.
Since gas floats on water, get a clear dip tube and put it straight into the tank to the bottom and place your finger over it and remove and hold it straight up, then put another finger over the bottom of the dip tube. You should be able to see how much gas you have floating on how much water and possibly even how much little bits of crap are in the bottom of the fuel tank. Use a siphon tube connected to a dip tube and siphon/pump out as much of the water in the tank as you can while not removing the gas, you may also get some dirt which is a good thing. I have not had to do this but have looked at our tank and think it is possible. Don't know about your tank design and there may be other water drain access/options on your tank.
I would taste a tiny bit of the water removed from both the tank and fuel/water separator to see if it is fresh, salt or brackish water. You can probably even have it tested. If it is fresh or mostly fresh (which it should be) it is likely condensation but if there is a lot of it that could indicate rain water and perhaps a little sea water spray getting passed a bad seal on you gas filler cap assembly. I had this happen a little once with a very old filler cap assembly, replace it with a new assembly or at least replace the seal to be sure, especially if it is old or shows signs of leaking and they also are cheap. In my case the whole assembly was replaced. Don’t forget to hook up the static discharge wire to a metal fuel cap assembly.
If this does not solve your problem you are now past my level of experience and need the advice of marine mechanics, for things like bad water sensors, computer problems and possible issues with tank overfill line one way valves (very unlikely) and other causes I have no clue about.
PS - if your Merc Motor is designed the same as the big older Opti, the lower motor assembly has two drain tubes with one way check valves (little balls) in them that goes through the motor plate the lower cowling joins up to. These tubes and valves are designed to drain any rain/more likely sea water that gets inside your upper cowling assembly out of your motor. They get clogged up with dirt, grease and paint chips etc very easily and then the cowling can hold lots of sea water in for long periods of time. It drips out slowly but may stay their too long. This can cause a lot of preventable corrosion on a warm motor and lead to things like lower motor cooling fittings failing. Don’t know if this could somehow cause your problem and think it unlikely, but in my view it is critical maintenance item to add to your list to prevent other serious problem from occurring. To check and clean them on our Merc OPTI you remove the upper cowling and the two sides of the lower cowling and pull out the two drain tubes and check and clean them. You should be able to blow air through them and the check valve balls inside the tubes should move freely. If not keep cleaning them until they do or buy new ones. I did have a dealer Merc mechanic tell me that they sometimes pop out the check balls especially if the motor is mounted very low to the water. This means that salt water can get splashed or forced up the drain tubes into the motor compartment but also drains out quickly. I think they are there for a reason and it is best to leave them but also to check them frequently and keep the tubes and the check valve balls working freely. As I said that is on an older OPTI and on your 4stroke It may be different but worth checking out. Look up a parts diagram of your motor on line to see how you’re motor is designed to drain off water that gets inside the cowling, if it does at all.
Hope this helps and is not a lot of things you have already done.