POSSIBLE ECU MALFUNCTIONS
Here are my findings:
FUEL:
The very first starboard 16oz sample I pulled out from the fuel line had in fact a small amount of water in it. The port 16oz sample had nothing inside, the next day to confirm I took out 2 litre soda bottles worth of fuel and after sitting for 24+ hours there has been no discovery of water or phase separation. The boat has been level on a trailer. I guess the marine 360 needed some time to get to work? Also I am assuming the majority of water had been used up by the engines while I was trying to start it on the water the day I noticed problems and the second day when I was running it a few rpms above idle in order to gauge what was wrong. When I arrived to my warehouse outside I started up the engines to take out the water in the coolant lines and pumps before I take it inside and they fired right up and didn't die on idle.
I'm going to try to take out the fuel pumps and seal them up because I believe that's where the water got in.
I ordered 2 water fuel seperators and will install them tonight for each engine
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FUEL INJECTORS:
They were pretty clogged but once I cleaned them with carb/air intake cleaner the spray was much more atomized. Resistance check and ohm readings were at 12.3, so within the 11.5-12.5 ohm threshold as stated in the service manual. For all of the connectors there was 12v power and ground when the key is turned to the on position, as well as barely noticeable flickering of my led test light when the engine was being cranked.
SPARK PLUGS:
I removed spark plugs from both engines and they looked fine because I put them in 3 months ago and they are the ngk irridiums although there was signs of a little bit of rust on the threads and the coil packs are a little rusty as well. I re-applied anti seize and dielectric grease, while reinstalling the coil pack I tightened the screw too tight and it broke while inside the head..?
MOTOR OIL:
I took out 2 water bottle samples the day this happened and it's been about 48 hours, the port sample is dark brown and the starboard is darker brown with a slight hue of green and a slight odor of fuel. I drained all the oil from the engines first with a hand syphon pump then by taking out the drain plug behind and below the engine, such a pain to get to that drain plug bolt with no mirror and only a smartphone camera but I drained it and ofcourse I managed to spill some in the bilge. Collected a little over 4 quarts total from each engine. New oil added is Mobil one 10w-40 with mobile one M1-110 filters. I have added only 3 quarts right now and will probably crank the engines to cycle the oil and slowly add half a quart more until the oil level is at the E mark when cold so that I can start the engines to see if my repairs have worked.
ECU'S:
So when I opened up the boxes for the ECU's there was no visible pool of water or rust but there was a very thin film of moisture on the rubber seal that holds the ECU box together, this film of water was present in both boxes. I'm assuming there was moisture buildup inside the ECU box and since the boat has been sitting in my warehouse while it's 80° out the moisture was finding it's way out. I unplugged the ECU and the connection was fine, no signs of water in either ECU connectors. To be honest the inside of the ECU boxes looked brand new especially the connections, as a matter of fact the inside of the ECU boxes is hands down the cleanest part on the boat I've seen. In any case I took the ECU's home with me and I'm going to attempt to dry them in case any moisture got in by keeping them in a container full of silica gel desiccant packets to dry them out for a day or two.
Hopefully these repairs I'm making will resolve the issue, I will make an update in a day or two once I put everything back together
I am grateful for everyone who took the time out of their day to help and give me advice, any more suggestions or tips would be appreciated ?