There is something else to consider when it comes to these supercharged boat engines with intercoolers regardless if they are SHO, SVHO, or even aftermarket units. This problem is something Yamaha did not consider since all the test boating is done in the North on cold clear water lakes. Dealers never see the problem because they use brand new boats or just take your boat for a quick spin and say they couldn't find it.
This condition is scale buildup, which is detrimental to any heat exchange system. The scale is composed of microbial/tiny marine life, and minerals present in any body of open water. Heating action and water flow cause deposition on the water side of any open water heat exchanger when it exceeds roughly 140 degrees Fahrenheit. As most of you probably know, the water coming out of our intercooler pissers can go well above that. And that's after 5 feet of hose as well.
When the intercooler can't bring charge air temperature (this is the temperature of air at the throttle blade as measured by the BAR Map sensor) low enough for the engine to safely use it, the computer steps in. It lowers AFR by injecting more fuel to cool the air charge, this causes power loss and increased fuel consumption. It also pulls timing to prevent knock or pre-detonation, again lowering power. And it lowers max rpm to reduce boost level, to subsequently reduce air heat up, to subsequently reduce charge air temps to safe levels. Power aside, RPM is thrust, thrust generates velocity. Velocity is what all this about.
This problem is exactly why that first time you took your boat out it ran like a raped ape, but then it got slower the next time and then slower again. Until the scale had covered every surface of your intercoolers water side, and you were left with a level of performance that is simply unacceptable. You probably never noticed because you had friends or gear or rough water. Or in my case, BEER! It may be that the first lake you went to was a glorified mud hole and you NEVER saw full speed once your break-in was done.
The simplest description of what is happening is that you are literally cooking microbial marine life to your intercooler and forming a calcium scale layer over what is supposed to be your main heat transfer surface. We ex-navy engineering guys call this a crud layer.
The speed at which this scale forms is dependent on water exit temp (How hot it got), water mineral content (how much crud there is in the water), the size of the water channels in your intercooler (clearance), and the amount of time the scaling threshold is surpassed.
This layer can drastically hinder heat transfer. Instead of copper or aluminum being your main contact point with the water, now it must go through another solid boundary with a much lower thermal conductivity capability.
Flushing with hose water after you trailer the boat will NOT remove this scale.
The hotter the air, the hotter the water gets. More boost creates more heat, that means that this will eventually become a problem for any boat intercooler using a raw water system that heats the water past that critical point.
How to fix it? You can remove and descale your intercooler with a descaling agent. You can also disconnect the water lines and recirculate a descaling mix using an external pump.
How to prevent this? The only thing you can do is reduce the peak temperature of the water coming out of your intercooler. That means for a given heat load, you must either use colder water, or increase water flow. Since I haven't seen a thermostat on a body of water yet, and our boating season is short enough as it is, that just leaves increasing water flow as a viable option.
Before anyone says, "Just add a bigger intercooler", that can actually speed up fouling. A bigger or more effecient intercooler is transferring more heat to the water - increasing water temp, and thereby the rate at which scaling ocurrs. It wont show up right away on a bigger intercooler because it starts off clean, and there is naturally more surface to foul before it becomes an issue, but it will happen.
By adding a dedicated intercooler line, you can drastically reduce the amount of heating action occurring in the water. It's simple, takes maybe two hours plus curing time for the through hull connection. It costs about a hundred bucks. If you feel frisky, you can even add a hi-flow strainer for another 40 dollars.
The benefits are not just limited to preventing scaling. The line helps compensate for high air and water temperatures which are factors beyond your control.
By adding the line, not only do you drastically reduce or completely eliminate the scaling problem, you are minimizing the temperature of your charge air, which means you maximize available power, minimize fuel consumption, and ensure the boat meets the performance levels you were promised by the dealer.