Have you replaced the factory intercooler hoses (yet)? If not, that would be the first place I'd look, starting with the driver's side.
Remove the sensors, pull the air cleaner up, unscrew the hose clamps front and back, inspect the hose thoroughly. Any splits can be temporarily repaired with gaffa tape and cable ties. The more the better!
If it's the fuel filter, pulling it is a pain. If it's the same as mine it will be clamped to the bash plate. Loosen the 3 bolts on the plate for better access. Unplug the sensor, then pull its retainer clips out and work it around behind the filter until it's hanging free.
My filter was on tight as hell, so loosening the clamp made it impossible to get enough leverage between it and the thing it screws into (which hangs free if you unclamp the filter). So I used the filter bracket as a ratchet: loosen the front of the bracket, rotate the filter 1/4 turn, tighten the clamp, then turn the thing that it screw into. Repeat a bunch of times.
Once it's loose, undo the bracket that holds the filter, get your head out of the way (or leave it and get an ear full of diesel - ask me how I know), point the filter at the ground and remove the water drain plug. Once it's drained, remove and replace the filter.
Good luck this morning, hope you work it out and get back on the road soon.
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