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Discussion Starter #1
I have a 2002 yamaha 25hp 2 stroke 3 cylinder 
Here's what's going on
I run the boat about 10 min to my fishing spot and turn motor off Runs good . Start motor again and probably run for 3-5 min and then it boggs down feels like it's dropping a cylinder. Sometimes I can turn motor off and back on then it will run a little longer before it happens again.  thoughts?

Carbs have been rebuilt
New tank, lines and connectors
Compression is 150 on all 3
Plugs are not wet 
Not overheating
I use 100/1 ratio
Help please.  Thanks in advance 
 

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I have the same motor and it had a very small hole in the fuel pump diaphragm and it caused the same type of problems. It ran good at idle, but it wasn't getting enough fuel and it would fall on it's face under load.
 

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Discussion Starter #3
Thanks for replying I have pulled the cover off the fuel pump and there was some gunk in it so I cleaned the best I could but I couldn't take the whole pump off the carb. How do you take it off?
 

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It's a part of the carb float bowl. The black plastic center piece is all you need to work on. http://www.boats.net/parts/search/Yamaha/Outboard/2002/25MSH3A/CARBURETOR/parts.html
 

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I have a 2002 yamaha 25hp 2 stroke 3 cylinder 
Here's what's going on
I run the boat about 10 min to my fishing spot and turn motor off Runs good . Start motor again and probably run for 3-5 min and then it boggs down feels like it's dropping a cylinder. Sometimes I can turn motor off and back on then it will run a little longer before it happens again.  thoughts?

Carbs have been rebuilt
New tank, lines and connectors
Compression is 150 on all 3
Plugs are not wet 
Not overheating
I use 100/1 ratio
Help please.  Thanks in advance 
Check your fuel bulb. I had the same exact issue every once in a while with my 60, could not figure it out for the life of me, did everything I could think of, and sold it with the issue. I contacted the new owner a few months later and he said that simply changing the fuel bulb solved the problem.
 

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Does it continue to run after the problem shows up? Maybe it's going into limp mode? Are all of the cdi connections clean? My 30hp had a few that were corroded really bad including the ground when I bought it.
 

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If your 100% sure that the carbs, fuel pump are good than I would start trouble shooting the ignition. I did manage to foul a plug on mine from idling a bunch and it caused the motor to act up. I thought the carbs were dirty for sure so I rebuilt them and all three looked perfect. $11 for three new NGK plugs did the trick.
 

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Discussion Starter #13
Had the carbs professional done getting rebuild kit for fuel pump tomorrow. New plugs. I think it's either the coils or power pack
 

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Had the carbs professional done  getting rebuild kit for fuel pump tomorrow.  New plugs.  I think it's either the coils or power pack
yes its 13 years old.... start replacing parts.

when my 1998 mariner started acting wierd this is what i did.
coils / stator / trigger / plugs / wires / etc.
these parts get brittle / burnt
heat / vibration will make things change (elect) after warmup.
 

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Living & Dying in 3/4 Time
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Probably a coil or stator. When they get old, cranky, worn, and hot, they start to short out.

Where is Brett? He can explain this much better than I!
 

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If it ain't broke tweak it a little....
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Make sure all bolts in your throttle linkage on starboard side of motor are tight. When I purchased a used 2006 25hp I went thru carbs, installed new plugs, cleaned fuel filter and installed new Yamaha fuel line assembly that terminated into tank with a brass 90 fitting and hose clamp. Ran awesome for a couple months then developed a similar problem to yours. I had the bolt that goes through the accelerator arm loosen. The motor would rev up in gear get on plane and the bog way down. Wait a couple minutes the back to WOT then bog down. Looked motor over real good and found loose bolt. Cleaned and reinstalled with Blue loctitie. Maybe not your same problem but would not hurt to look.
 

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Discussion Starter #17
Thank you all that replied . I went through the fuel pump again and found a small hole in diaphragm. Installed a new one and gasket. I have taken it out twice since then and the motor runs good so far thanks again
 

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Sweet! Keep an eye on the thermostat. Mine had all kinds of trash caught up in it. I check it often now. I used grease on the thermostat housing gasket to prevent it from sticking so that I can re use it. It seals just fine.
 
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