jm. is right, you need a manual to help figure out the fuel system piping. Some systems go from the tank to filter to transfer pump to injector pump. Other systems do go from the tank to transfer pump to the filter then to the injection pump which provides high pressure fuel to the injectors. I see a hand primer pump on your transfer pump so I think yours goes to the transfer pump before it goes to the filter. However I can't say that your hoses are all there or connected properly, especially since you seem to have a loose hose. There is usually some return piping to the tank, for excess fuel, but I can't say on yours, some else may know what and where it is.
To be clear the main injection system components are the injection pump which sends the high pressure fuel to the injectors and the injectors which spray the high pressure fuel into the cylinders. It will help people understand what you are talking about if you learn and use the right names for the components. So if you took the injection system to the shop I would expect you took the injection pump and injectors. I am thinking they told you the injection pump had water in it, not one of the injectors, which you would have had to pull out as well.
The fuel bowl, as you called it, is the fuel filter housing that should have a cartridge type filter element inside it. You need to change that element and clean that housing. If you have water in it, you may need to drain the fuel tank completely and start with new clean fuel. Either way I would recommend getting a couple filter elements and changing it regularly, to protect your fuel system.
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