You need to start from the fuel tank, and work towards the injectors. Verify you have fuel at the outlet of the lift pump when the key is switched on. Once that is verified, follow the line to the fuel filter. Make sure the filter is getting a good flow of fuel at the inlet and outlet, once the fuel filter is replaced. Crack open the T-valve on top of the motor, and make sure you have steady fuel flow when the lift pump is jumped. You should have a good, strong fuel flow from the vent line (not just a trickle). Once you are 100% sure the injector pump is getting a steady flow of good fuel, you can move to the injector pump.
In essence, you want to start with the simple things first. Make sure ABSOLUTELY EVERYTHING in your fuel system is functioning correctly before you start throwing other parts at it. Injector pumps aren't cheap, and you want to take good care of them. My bet is that you have filled the injector pump and the associated lines with water, and the injector pump won't pump it as well as the diesel fuel. You need to start with what you know. You know that the water-in-fuel light came on. That is caused by water build-up in the water/fuel separator (inside of the fuel filter housing). Get rid of the water, and make sure there isn't any more water before you move on.
As far as getting a watery fuel mixture out of the pipe, don't plan on it. Just think of how much fuel/water would have to pass through the motor to reach that point. Generally, you will see a white/greyish smoke coming from the exhaust during cranking when there is a low fuel scenario.