Hi Nicholas!
The DP chip just increases the fuel, if the cost was similar to the ChipIt chip I'd go to ChipIt. The 3" exhaust will give you some improvement - although the effect SHOULD be minimal, enough people have come forward saying their 3" systems provide extra power. I'm not sure if dollar-for-dollar the power increase is going to be the same as the chip - I think the chip would win easily.
The D40s have front-mount intercoolers and we have no trouble wading through creeks and rivers with water up and over the bonnet. The intercooler actually performs better when it's wet, and there are companies that manufacture water misting systems to spray a fine mist of water on the intercooler. So the answer is no, it won't stuff things up by submerging it!
The snorkel has a lot of value, but get the guys to install it and test it - you should be able to stall the engine by placing something over the snorkel's intake. Drawing air from higher up, the particulates in the air are smaller and less concentrated. The air is cooler, not coming from the hotter areas around the engine - the cooler the air, the more oxygen molecules per cubic centimetre, which is just adding to the bonus given by the intercooler.