I have been going to post this topic for a while - it's a good one.
I haven't set up a factory ECU in a boat but from my Autronic experience, these are a few issues you will need to deal with.
I run an Autronic SMC Marine version which is fully waterproof. You can chuck it in a bucket of water with the engine running and it wont stop.
Factory ECU's are much cheaper and you get perfect tuning for normal engine running and economy, plus faultless starts. All still possible with aftermarket, but can require a lot of tuning hours!
Factory ECU is also suitable for forced induction, which is nearly essential on larger or fast boats. Not sure how much boost the factory ECU can support.
O2 exhaust gas sensors don't like water. Full stop.
I believe some versions of the ECU use 4 sensors and some use 2.I'm not sure if the factory ECU can be run without them? Rod or KDog would know??
If you are injecting water into your exhausts to cool them and quiten the engine exhaust note, you will run into problems. The o2 sensors have a ceramic part in them and once they are hot, any water that gets on them will crack the ceramic bit and the sensor will be stuffed. I have seen water injected downstream of the sensor to try to get away from this problem, but with limited success. Sometimes when you pull up in a hurry - (fallen skier ect.) water will rush past your exhaust flaps and run up your pipes. Also a coughing or backfiring engine can do weird things and suck injected water the wrong way. You can also run dry pipes in a race boat to get around this. Personally, o2 sensors are for economy reasons and you don't need to run them in a boat. I bolt on a dry pipe for tuning and put a o2 sensor in that, then remove it once I have finished tuning.
Next issue is keeping everthing simple. With the factory ECU you will need to plumb the Mass air flow sensor (MAF) in front of the throttle body. This takes up room under a tight fitting engine cowl. Aftermarket you just run on manifold pressure which you don't need a MAF.
Not sure how many other things are necessary to run the factory ECU wich would clutter up your engine bay. Also remember that every less piece of wiring or electronic sensors or connectors is one less thing for water to get into and give you a great day rowing home. From memory, my Autronic runs 16 general sensor / output wires and 9 injector wires.
It connects to water temp sensor, 1 cam sensor, crank sensor, interface box, 2 ignitors and the injectors. Probably as simple as it gets except for the interface which is necessary.
In conclusion I felt the Autronic was practicle and good value at the time and I am happy with it.
On the other hand, there is a lot known about the setting up of the factory ECU's nowdays and if they can be made to work, you cant beat them for value and engine smoothness ect.
Look forward to replies for solutions to fitting the factory ECU, escecially the o2 sensor issue.