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Starboard pistons very hot, port side cool

Monomotapo

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My 2000 model 225hp EFI 3l V6 is running rough. Recently replaced thermostats, but starboard piston heads too hot to touch, while port side can keep holding fingers there. This is after idling for 5 minutes with running the revs up and down occasionally. I have read that if a coil is malfunctioning it causes two others also to malfunction, but is this all on one side or opposing pistons? Regarding rough running, engine was having fuel bleed line problems and backfiring/missing and I suspected lean running. I cleaned injectors, checked for spark and ensured intake gaskets had good coating of gasket goo. Back firing seems to have been resolved, but still running rough with intermittent loss of power on higher revs. Any help gratefully accepted.
 
Thank you for responding, Faztbullet. I replaced the thermostats with new ones (don't have the serial#), but the covers are originals and I am not sure what you mean by the 130 d. t-stats?
 
He means the TSB from Merc. calls for installing updated thermostats w/a temperature of 130 degrees F.
 
Sorry about taking so long to reply and thanks for your help, too, Guyjg. My model is a year 2000 and from what I have been able to ascertain, the thermostats should engage at 143degF, whereas the TSB 2002-08 is an upgrade from 120d. to 130d.F. for later model 225EFIs (s/n OT409000 upwards, I am OT108729). My replacement thermostats are only a few hours old. You are on the right track, though, because one thread I read from Mercury said the colder running heads would foul the sparks, which seems to be what is happening because the engine will surge up and down when held at any given revs and it runs rough at idle. This might also account for the backfiring I was experiencing and the fuel bleed lines popping off or splitting. Any other thoughts very welcome.
 
Check the temperature sensor connections for corrosion. If none is found get the engine scanned to see what the sensor is doing. If it's malfunctioning it can cause the engine RPM to oscillate. You might remove it to see if it is coated w/mineral deposits. Since one cylinder bank is hot to touch it may have a water jacket blockage. Has the impeller been replaced recently? Was the old one intact? If not there may be a chunk of it impeding water flow. Are you running in saltwater? It can cause a builup of mineral deposits in the water jacket. Pull the cylinder head and look at the water passages.
 
Thanks again guyjg. I will do as suggested and check the temperature sensor. The water pump impeller shouldn't be a problem as it is relatively new only having run a few hours. It is in saltwater but gets a thorough flushing with fresh water after each run. I will remove the thermostats for checking. I would still be interested to hear whether a faulty coil could effect the performance of two others (out of a total of six) and whether this would happen on one side of the v6 motor only (i.e. port or starboard) or whether the two effected coils could be on opposing sides? Thanks.
 
My Merc. service manual states: "A shorted STOP DIODE in any one CDM will prevent at least two other CDMs from firing." Each CDM gets its charging ground path independently through the stator's white leads. First of all you need to check the spark from all CDMs using a multi-point spark gap tester set at 7/16" to compare each against the other. Pull the elec. plugs off each one and examine it for corrosion and straight pins.

A non firing cylinder isn't going to cause the heat issue you have in the cylinder bank. A lack of or reduction in cooling water flow is the problem. Pull the head off and you'll find alot of mineral growth in the water jacket. Flushing w/fresh water after each use helps but should include flushing w/a salt neutralizing solution.
 
Thanks again Guyig and sorry to bother again. I removed the thermostats and tested them and they worked fine. I blew down their housings into the water jacket and could not detect any resistance. I am getting a very strong jet from the tell tale and it is relatively cool. Checked the temperature sensor connections and tried to remove the sensor, but it appears to be corroded in. I did a visual spark inspection and a couple of them seem to have a very brief intermittent loss of spark. Could a coil (CDM) or two be failing but still mostly produce a healthy spark? A further pointer is that I am getting excessive exhaust smoke (like fuel/oil is only partly combusting) while running it at higher revs with hand throttling and its definitely not firing on all cylinders (seems to do a bit better at higher revs). Perplexed to say the least!
 
...a couple of them seem to have a very brief intermittent loss of spark. Could a coil (CDM) or two be failing but still mostly produce a healthy spark?
Anything is possible. Verify the grounds for the coils are clean and shiney....sand them. Recheck for good spark. If the spark is questionable troubleshoot the coil packs and replace them as needed.

Maybe someone else will chime in here about the high head temp on one side...YES, Merc. refers to them as cylinder heads in their manuals.
 
These symptoms can also be caused by a dropped exhaust tuner.

Take off the leg and check the tuner is still in place, generally only happened on the 2.5 motors, but worth a check.
 
Thanks everybody for your contributions. This is the list of things "discovered" and corrected so far and those still puzzling:
1. Fuel injectors removed and cleaned 3x by me and then professionally cleaned. There were some problems here but I no longer believe fuel is an issue.
2. I noticed 4 of the timing ribs (not sure this is the best description of them) on lower flywheel or stator had some rust coating so I wire brushed them and painted them and then readjusted the stator (flywheel) sensor. This showed a remarkable improvement in the backfiring problem and fixed fuel bleed line leeks and ruptures, but still power on all cylinders came and went seemingly mindlessly and mostly only a few fired at a time.
3. Top starboard spark plug clip had recessed away from the spark cap so may have caused sporadic missing. Rectified.
4. Battery Positive Post butterfly screw while tight to the feel was not properly securing the leads which could be moved by hand. This obviously accounted for occasions with dead starter conditions. Rectified.
5. I read a post from Faztbullet (December, 2012) to somebody else's problems that the shift interrupter switch on the shift bracket kills cylinders 2, 4 & 6 (all my cool port side cylinders!) so I isolated the switch but still suffered uneven running (the switch still made a very slight difference even with the uneven running). With the switch isolated and motor idling (poorly), disconnected all the power plugs to the port side coils (CDMs) without discernible change in engine performance & then started doing the same on starboard side with engine dying after two disconnected. Moved all port side CDMs to starboard and vice versa, with identical outcomes to the above. So it seems there is not a coil problem, but port side pistons are not really firing consistently and at times, not at all. Yet on some earlier occasions (months ago) all pistons would fire fine at cruise speeds for probably 3-5 minutes and then the problems would manifest. I have not yet tried Magnum19s solution above regarding a dropped exhaust tuner, but could this be having such a dramatic affect on the port pistons, assuming starboard are still doing their job? I will be immensely indebted for the answer to this problem! Thanks.
 
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