For those that are interested, here are just a couple of reasons why too much cooling, especially in a supercharged engine that is tuned for running in a specific temperature range, can be a very bad thing -
Having built a supercharged engine or two from scratch, I imagine that Yamaha built a little more gap into the rings on these engines than a naturally aspirated engine would see. They definitely used a significantly lower static cylinder compression. That means that under the right conditions - prior to reaching normal running temperature - more cylinder gasses (not just fuel, water vapor also) will leak past the rings, and into the crank case, eventually ending up in the oil pan. That's OK....once the system does reach normal operating conditions, the engine oil should be plenty hot enough to vaporize off any fuel or water that does make it into the oil. Also once the engine gets to normal operating temperature, the cylinder leaking should be reduced to an absolute minimum. If the engine does not get hot enough to vaporize contaminants out of the system, cylinder leaking will continue, they will mix with the oil and a whole host of problems can occur.
Installing extra cooling ports on an otherwise stock engine that bypass the thermostat housing (or removing the thermostat altogether) will create a temperature stratification across the engine. That means that there will be some points that are significantly hotter than others. That means you get uneven heat expansion across sealing surfaces, unbalanced internal stresses on lots of parts like the block, the cylinder head, and who knows what else. Sealing surface problems can cause a blown head gasket, significantly different temperatures cylinder to cylinder can cause either a lean or a rich condition. Lean condition can cause pre-detonation (uncontrolled auto-ignition of your gasoline/air mixture) and catastrophic engine failure. Rich conditions will cause more gas in the oil and magnify the problems with contaminants in the oil system.
Something else to consider is that if the cylinder doesn't seal properly you can get oil in the combustion chamber. The common thing is that you foul a plug, especially if the cylinder was already rich to begin with. IF, however, the cylinder was lean to begin with and you now have 40 octane motor oil in the cylinder with 87-93 gasoline, you increase your chances of pre-detonation significantly.