What battery do you have for the R2.8?
The R2.8 is an unusual diesel engine in my limited experience. It has a lot of crankcase (I think that's the right terminology) pressure and seems to blow a fair amount of oil into my intake piping from the crankcase. I kinda wonder if you're getting some oil from there.
I have the same 3 year old agm battery that my 4.0 had, but I also have a 27 series deep cell battery for the rear winch that is wired directly to the engine starting battery. I did not route my crankcase venting hose to the intake tract, instead I routed it to the bottom of the radiator where it vents into the air. On occasion I smell some oil vapor coming from the crankcase vent, but it isn't terrible.