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Previously I was always advised to not use the 2004 Mercury 90 4Stroke flushing system to cool the engine if you have to run it out of the water (put muffs on the water intakes instead).

I now have the 2015 version of the same engine, and it has what appears to be a more sophisticated flushing system. In fact water comes out of the telltale when I use it - didn't happen with the old engine.

All I have to do is run it at idle for probably less than a minute to run the fuel out of the engine for storage (after disconnecting the fuel hose from the tank). This is recommended when ethanol is present.

There is no mention in any documentation of not using the flush attachment.

We're talking like 45 seconds here.

Any advice?

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If the engine is that new (under warranty) I'd suggest you speak to the techs at the marina that installed it to be sure you can use the flush port. Wouldn't want to see you do something that would cause issues later. I can run either muffs or use the flush port on my Evinrude (per the manual) but I typically use the muffs because I have them and it's quicker than threading a short hose onto the flush port.

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From what I understand, the entire reason not to run an outboard without water is to prevent damaging the water intake impeller. So my inclination, if the engine has to be started up, is to use muffs. This puts water over the impeller.

I have always understood that the external flushing connection is for flushing salt, etc out of the passages, but not for running the engine, even though there would appear to be adequate cooling water. On my Merc 200 EFI's, the hose flushing system does activate the telltale, poppet valve and thermostat, but water does not appear to be inside the water pump, hence the impeller would be turning dry if the engine was running.

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I only start my engines with water going to both the powerhead and the lower unit on my yamahas.

When I first get in I run the hoses on the powerheads (I have twins) for 15 minutes with the engines off. Then when I start the engines I do one engine at a time with two water supplies - One to the powerhead and one to the lower unit via the muffs.

I heard the same as Finnegan: the reason to run with muffs is to protect the impeller.

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OK, that makes sense (impeller damage). Water does come out of the intakes when flushing but that of course is the wrong direction so there's no indication it's going completely through the pump.

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According to my 2012 ETEC 90 manual you can run the engine using the flushing port but only at idle speed.

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Worked on it last weekend. When I use the muffs, only a few drops of water come out of the telltale; whereas, as I said previously, when you use the flushing port, the telltale runs strong.

I don't know if this is significant. I did use the muffs, but only to run the engine at idle before/after oil change and to winterize the fuel system.

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Is the hose on full blast? If it is, you may have a partially clogged line. Try some trimmer line into the end of the tell tale. Often there is a gob of crystalized salt just at the end of the hose/fitting.

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Phil for what it is worth I have now taken to pulling the thermostat off my 2 stroke Yamaha about every other outing. It is shocking how much salt and sand I find built up. A thorough cleaning and blast of air takes less than 30 minutes. The thermostat cover gasket on my Yamaha is inexpensive and knowing that I have a forceful tell tale is very reassuring.

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My pee tube gets some sort of critter/bug that wants to build a mud like home in it from time to time. I keep a thin piece of copper wire in my tool kit and run it in 2-3" and it clears it immediately.
Another good way to see if the water pump and impellor are working well is to put muffs on and only a minimal flow from the hose. Have someone start the motor while you watch the muffs. If all is well you will see the muffs suck in as the water is pulled into the cooling passages. Not recommended for anything but testing.

I am almost afraid to post this, but in response to Yamaha 2-strokes and water flow: I owned a 1985 70 HP Yamaha 2-stroke for 25 years, almost all of it entailed a long crossing of our muddy and salty and sandy creek to reach good water. At high tide I would let the motor stay all the way down to dredge a deeper channel at times.
Seven years ago the lower end was sheared off on the remnants of what was probably a submerged duck blind.
My used replacement lower end was welded in place, so impellor and pump were untouched for at least 5 years until I sold the motor.
Yes I told the buyer of this and all other facts including the time the motor hung submerged for 3 weeks when the stern cables broke and the bow was held high through all those tide changes. That motor never had a water pump or thermostat replaced ever.

Most dependable motor I ever owned.

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Though this is something that I preach but do not practice. ...some things are best left alone. My 1991 Yamaha 40hp impeller was not changed for 20 years. Looked new when it came out.

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Swist -

I re-read your original post and am really confused. Are you saying that the Mercury manual says to drain the motor of fuel completely when ethanol-blended fuel is used? This seems stupid.

I ran a 4 stroke, fuel injected motor with blended fuel and never ran it dry. For 7 years, not an issue despite -10 degree temps for weeks in the winter.

On the salt build up, I always ran the motor a good 15 minutes on the muffs. Spent the time cleaning and offloading.

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The owner's manual recommends draining as much gas as possible from the fuel system (engine, lines, tank) if there is ethanol in the gas (page 84, 2015 manual).

HOWEVER, my Mercury mechanic, with whom I would trust my life says to take the external (Racor) filter bowl off, empty it of gas, and fill it with 1/2 Stabil and 1/2 best quality TWO CYCLE oil, then idle the engine for a few mibutes. Then drain the tank (put it in the car), but leave all else alone.

So that's what I did.

BTW, Saying a procedure is "stupid" does not lend itself to intelligent discourse in this forum. If you disagree, say so and then explain why in an objective tone.

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My thinking is the components of the fuel injection are in a closed system and under pressure. Evaporation is not a factor. The gasket materials may suffer if subjected to air (if drained).

While adding Stabil or other similar product is a good idea in a fuel system that is open (vented tank) to the air and evaporation. Once the fuel is past the low pressure pump, it is in the closed portion of the fuel system.

What would the mech say to the comment "I would think adding 2 cycle oil would clog the fuel injectors, VST and fuel filters"

Professionally cleaning injectors via Flagship or other vendor runs > $50 per unit.

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I hear you, but this guy has never led me astray in 10 years. I think he said it was sort of like "fogging" - getting some oil on components which might corrode. There's probably about 2 tablespoons of 2-cycle oil involved and if it clogged the injectors I would have noticed when I started up after that treatment.

I also admit I can find no reference to this procedure anywhere else. So I don't doubt your skepticism; however, I gotta go with my guy.