2006 Mercruiser 5.0 2bbl Misfire/stumble once warm

65SlvStang

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Jul 7, 2025
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Hello, I have been struggling to find the root cause of a misfire/stumbling issue on our 2006 Bowrider. Boat has ran flawlessly for us for the last 10 year or so past normal maintenance items. This year is the first year we have run into issues.


Symptoms:

Boat starts right up when cold. We have had the boat out 3 times now this season and all 3 have the same symptoms

We unload boat off the trailer, idle around for driver to be picked up at the dock. We cruise WOT once warmed up approx 6-7 miles down the lake idling trough 1 no wake zone. No issues run at all during these periods. No stumbling, misfiring, etc. Speeds are in normal range for our boat 40-44 mph based on qty of passengers.

Once we stop and float for a while, could be 30 min, could be 3 hours. The boat is extremely hard to restart. As it is cranking you can hear/feel the engine trying to turn over. After 4 or 5 5-8 second cranks the motor will turnover. Seems to idle OK and giving a throttle blip in Neutral gives a quick acceleration with no misfire or sputtering.

Once we idle out of the no wake zone and start to roll into throttle we instantly start getting a miss/sputter or misfire. To the point where we struggle too, or can't get up on plane. While pushing into throttle approx past 30% is when we start to get the misfire and what sounds like a backfire or detonation (Can't tell). Reducing throttle 5% or so will stop the misfire. I can ease back into the throttle again and sometimes it will accelerate and can get on plane, sometimes we can't it is very intermittent of the amount of throttle I can push it before it starts to misfire again. The last trip out I was able to feather the throttle back and forth for a few min and got the boat on plane and ran out to about 30 mph. Enough to make it to the bock area. Once we got there and came back to idle, I ran into the same issues where anything more that 1200 rpm it will start to misfire again. So far it has never stalled on me. Any when cold always fires right up and will run fine for a bit.




Boat:

2006 Bayliner 225
Mercruiser 5.0 2bbl
130 hours
Last years winterization was 50% fuel take with Staybil
RV Antifreeze once thermostat opens and fogging oil oil
Dewinterization was Oil change with New filter, Fuel/water separator filter
Filled the rest of the gas tank with fresh fuel (89 octane, same I have ran for 10 years)
Generally winterize around Oct/Nov and dewinterize around April/May


History:
Every year oil change
Impeller every 2-3 years
Full tune up (Plugs, wires, cap, button) 3 years ago


Troubleshooting:
Initially it felt like fuel starvation so I did replace the fuel/water separator again - no change
I then though this may be electronic related since it only happens once the motor gets warm so replaced the Coil - No Change


Next Steps:

I am struggling with next steps as I can't really determine right now if this is a fuel or ignition related issue. Looking for feedback from anyone else that has ran into this issue.

Based on reading through the forum it sounds like I should be looking at fuel pressure/delivery to the carb. I do have an electronic fuel pump that mounts towards the front of the block on the starboard side right above the screw on fuel filter.




Looking for any feedback or suggestions.
 

alldodge

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Mar 8, 2009
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42,957
Welcome
Happen to have the motor serial number?

Being a carb and what your saying I'm still thinking fuel, but could be something is getting hot just sitting

If you can put a fuel pressure gauge between pump and carb. You should get 4-7 psi from idle to WOT.

Could also put a vacuum gauge between fuel tank and filter. Should not get over 1 inHg
 

Scott Danforth

Grumpy Vintage Moderator still playing with boats
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Jul 23, 2011
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does your ignition trigger have the older 2-wire sensor, or the updated 3-wire sensor?
 

Scott06

Admiral
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Apr 20, 2014
Messages
6,977
does your ignition trigger have the older 2-wire sensor, or the updated 3-wire sensor?
2006 will be 3 wire, but doesnt mean the sensor isnt bad.

Agree with check fuel pressure. Would be interested to use a spark gap tester when cold and after sitting hot.

Would also check to see if fuel is leaking into intake after shutdown and choke is fully opening. What do spark plugs and inside of cap and rotor look like ?
 

65SlvStang

Recruit
Joined
Jul 7, 2025
Messages
3
Welcome
Happen to have the motor serial number?

Being a carb and what your saying I'm still thinking fuel, but could be something is getting hot just sitting

If you can put a fuel pressure gauge between pump and carb. You should get 4-7 psi from idle to WOT.

Could also put a vacuum gauge between fuel tank and filter. Should not get over 1 inHg
I do!
Serial number is 0W623327
Family 6M9XM05.02VC

I will need to grab a fuel pressure tester, but that would make sense.
 

65SlvStang

Recruit
Joined
Jul 7, 2025
Messages
3
2006 will be 3 wire, but doesnt mean the sensor isnt bad.

Agree with check fuel pressure. Would be interested to use a spark gap tester when cold and after sitting hot.

Would also check to see if fuel is leaking into intake after shutdown and choke is fully opening. What do spark plugs and inside of cap and rotor look like ?
I have not pulled it apart yet and boat is about 1 hr away at the moment. But will verify shortly. According to parts lookup it "SHOULD" be a 3 wire.
 
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