I have an idea of what to check. You said you are getting no cooling water pissing, and your leaking water into the hull. Plus your cooling lines are all screwed up. I bet your lines arent hooked up in the back properly either. Sounds like someone just stuck them on whatever they reached.
Stock exhaust uses the "unused" fitting as an extra water return. It spits water out of that fitting. Modified exhausts often do not use this line at all, and you may find that someone blocked it off on the inside, possibly by putting a bolt in the hose. There is another cooling line that comes in right next to it, and that should be hooked to your exhaust manifold, just beyond where exhaust exits from the cylinders.
If somehow someone switched the two ports on the inside - easy to do - you may have the lines hooked up to the wrong fittings on the inside of the hull. Your engine would not be getting any cooling water, which would make it get hot really really fast. DO NOT run your engine for more than a few seconds until you have your pisser working. You may have already done permanent damage.
Check to make sure that each of these fittings on the inside of the hull is connected to something. If a line was loose, water can come in, and go out. Make sure that the hoses are hooked up to the right fittings. On the inside of the hull, you should have one line that goes into a dohickey (check valve) and then down to a little plastic box with a bunch of holes in it. That is the stock bilge. It only works when your motor is pushing. On the outside, this line will run at an acute angle to your pump. You will have another line tapped into the side of your pump at a right angle. This one provides cooling water to the motor. Blow through it and make sure its clear. Also, make sure you know which fitting/hose it goes to on the inside of the hull. That line is the one that goes into the exhaust manifold, right where it bolts on to the cylinders. Cooling water from this line goes through a water jacket in the manifold, and into the cylinder block, right around the actual cylinder sleeves. Then it goes up into the head and out that u shaped hose, back into the other part of the exhaust mani. It runs through a water jacket to the other end of that manifold, where it sprays into the part of the exhaust that has the hot gasses. It also comes off from this point to your "stinger" and your pisser, as illustrated by wilke.
The stock system has one more fitting that comes off and goes out the back, but that usually is not used in aftermarket systems.