Friend of mine's boat. It will run fine all day long and then the next day it may run and just randomly start backfiring on Port side. It will just pop and Crackle and start lose rpm slowly, you can take the throttle and jacket and pump it to try to keep it running it may come back but most times it will just die. You can always get it started back up and it will idle fine and once you start to put it under load it'll start backfiring again. Then I would say after about 10 minutes of trying to keep it running all of a sudden it clears up and runs fine. So of course every time he takes it to the marina it's running fine and they can't find anything wrong with it this is been going on for three years. I thought I would try here to see if there is any ideas that could be lended.

How does the transom look? Is there any black soot? Sounds like a carburetor running rich fouling the plugs.

It's fuel injected it doesn't sound like it's backfiring threw the exhaust it sounds like the induction backfire. Back of the boat is clean.

Fuel pressure dropping? Ignition module on its way out? Start with the cheap stuff.

I just had to put a new fuel pump in, had the same symptoms.

I agree sounds like loss of fuel pressure and that backfire and rpm loss is the knock sensor doing its job. I had a very similar problem on my 575sci and it turned out to be the lift pump

Just went through this with my 500s, ended up being a bad coil.

A mechanic friend of mine had the same symptoms on that engine. After lots of diagnosing and testing, it turns out the spark plugs were the cause.

Lots of suggestions on here...I'd start by putting it on the scan tool to see if any codes have been thrown. I'd also probably put it on the scanner while running to see if any of the parameters are out. Finally, if nothing shows up, I'd start swapping parts with the other engine to see if the issue follows. I'd start with the coil...it's easy.

As crazy as it sounds, I'd watch the engine temp very closely. It can increase due to low water pressure, especially if he is trimmed and running shorty lowers. The engine temp will increase, but not to a point that it throws the alarm or a code. Once this happens, it causes the ECM to start adjusting. Mine was doing the same thing, with the same symptoms. One the engine cools a couple of degrees, all is good again.

Had a problem like that on one of my boats also. The coil had a hair line crack and would seal or expand based on temperature or vibration. Never had a problem while trying to run engines on trailer but for some reason while underway and when it felt like it would happen. Try running the engine when dark and engine is hot look for electric spark leaks plug wires could also show sparks.