Yamaha 25 hp 4 stroke runs rough when warmed up

I have a used 2004 25 hp four stroke, manual start, tiller that I recently purchased knowing that it would need some work. Here is what has been done thus far:

by me:
New plugs
New inline fuel filter

At marine service:
Oil change in head and lower unit
New impeller
New lower unit gaskets/seals
Carbs cleaned

Compression is apparently good.

Mechanic says there are indicators that motor was run hot in the past.

Motor starts on second pull every time, idles smooth, but runs rough when warmed up. I have not felt if water from 'pee hole' is warm or not since it's been at the shop for a month. I got no straight answer on what they think should be done next. It has been four days since they even looked at it, and I'm just going to go get it tomorrow and try another mechanic. Thought it worth a shot to post here and perhaps get some ideas to try before spending more on labor hours.

With everything we have done to it, why wouldn't the darn thing just run like a sewing machine when warmed up? Thanks any ideas you can throw my way.

[boats.net]

It's hard to say probably start with carb sync and adjustments.

[robert graham]

if it runs smooth when it's cold(when the choke/mixture enrichening is on) and then runs rough when it's warm(when the choke/mixture enrichening is off), then it sounds like a lean mixture issue. if you have a manual choke, try opening it just a bit after the engine warms up to see if that smooths it out and if it does that will tell you that you probably need to have the carb cleaned, which will get your mixture at a normal richness at normal operating temperature. need to run a fuel stabilizer like Sta-Bil or Seafoam and install a fuel/water separator on your transom(Walmart- $25), easy to install. Good Luck!

update

I picked the motor up this afternoon, brought it home, and of course had to see how it ran.

She fired off on second pull like always. Idle was good, but rough with moderate throttle. I said what the heck, let Seafoam run through it for awhile. I have nothing to lose and the tank of gas with Seafoam mix is paid for. Neighbor came over (he loves boat motors), we talk, motor ran, we goosed it some, and after a while neighbor noticed that idle sounded better. We goosed it again and she did better. We just hung out and talked and let the motor run and it got better and better. After awhile it ran good enough that I would have taken it to the river had it not been so late.

I am optimistic that the Seafoam is making a difference. The water (it's all cool where it should be) on the ground has started showing carbon and light fuel on the surface which leads us to believe that deposits are breaking loose as she runs, and that may be partly why the motor is running so much better.

I am optimistic and plan to take the boat to the river tomorrow and just run it at different speeds and see if things hold up.

On a side note, carbs were cleaned at shop, I do have a water separator installed and will add Stabil tomorrow. Wonder if I should clean carbs myself after all this apparent breaking lose of things.

Thanks for the advice. Hope the darn thing doesn't catch on fire or sink the boat.

Some improvement

She fired up on first pull at river this afternoon. I turned up river with a light throttle and she ran like a sewing machine for about 30 seconds. I was happy. Then she started chuggling and that was all it would do above a light throttle. I slowly went up river, shut the motor off, and fished for awhile. I started motor back up and she ran like a sewing machine. I said, what the heck, and goosed it. The darn thing jumped up and almost planed out in no time, but right before plane she choogled again and sat back down. : (

Mech says compression was good. Is there a chance the powerhead is ruined? I think the darn thing is just gummed up/carbed up. It will rev up just fine in neutral even when warmed up. Wouldn't do that before I spend the money on servicing.

My next move is a Seafoam shock treatment.

update

It was a $30 thermosensor...

[Gannman87]

Having the same problem

I realize this is a very old thread but I am having the same issue out of a 96 Evinrude 25hp 2 stroke. When I say same problem I mean to a T!!! Everything.... Were you able to change the thermosensor yourself? I wonder if my motor has one of those..

[rodbolt17]

I can tell you a 2 stroke 2 cyl jonny/rude of that era does NOT have a thermosensor.
the subject F25 did not either.

I can say that SOME jonny/rudes of that size DID have a thermo SWITCH.

big difference between a SENSOR and a SWITCH.

easiest way to tell if your motor has it is to simply LOOK.

if the head has a tan/orange wire going into a switch it has SLOW.
if not it does NOT have any temp monitoring.

SLOW was the jonny/rude acronym for Speed Limiting Overheat Warning.
not all tiny mite jonny/rudes had it.