That looks a lot of water - and it's green which would imply growth of some kind. Keep that sample don't chuck it.
I'd be asking some pointed questions at the filling station - that is a lot to have leaked into the tank if it's not rusted a big hole in the top and let spray in..... either someones added that much or it's contaminated fuel.
Apologies it teaching to suck eggs...
To clear the system, dump off the tank as you have and drain the main filter, then prime from the hand lever on the lift pump. It'll take a bit of doing but it will go. If the pump doesn't prime keep turning the crank a quarter turn and try it till it does - the lift pump only works for hand priming when it's cam is in a certain position.
With a full filter fo clean diesel, connect it all up and then slacken the return banjo on the injection pump. you can then prime with the lift pump and blow clean diesel into the injection pump and flush all the crud out. refasten banjo, undo injection pipe tops, crank engine five seconds to flush the lines. Celan up spilled diesel, fasten up injection pipes and she should start....
