The wiring and plug going to the bottom of he fuel filter assembly is the 'water in fuel sensor'. It is very common to damage these wires and plug cos people usually forget to disconnect them before undoing the water trap to release water in the fuel filter. As it is a commonly replaced item Jeep supply a genuine replacement pigtail for about $60USD, can find it online. BUT, for me personally after mine got damaged I haven't bothered to fit the new pigtail cos the water in sensor is a joke and sets of the light on the dash after you have driven through a puddle or been through the carwash.
Replacing all the fuel lines is a good idea too.
Can add some TCW3 marine oil into your fuel to help further lubricate the fuel system espsecially when you run the engine for the first time after cleaning everything. I actually run 300ml of TCW3 per tank in my CRD anyway on a normal day to day basis.
Also, if you are not already, join the JK Wrangler CRD Owners group on facebook. Plenty of knowledge there for CRD's.
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