Alright, well lets get this out of the way now. The shop you took it to is NOT a good shop. That said yes you absolutely MUST flush the cooling system. The presence of detergent style (diesel rated) oil in a cooling system can and will deteriorate the hoses, seals and so on.
The FICM can be programmed, even if I can't do it I can walk right into the place a childhood friend of mine works at, install it on a truck and program it for YOUR truck. However...the step up board for the injector drivers is probably the culprit and this requires no programming. I would install a 53V step up board vs stock 48V anyways. Unlike alot of shops if I do find problems on the control board I can repair them rather than swapping boards since we are equipped for board level repairs at my shop.
The oil cooler is in the same location, however on the 4200 the only thing that has to come out is the downpipe. Even if the turbo has to come out its all right there at the top of the motor with easy access. The thing I have to stress here is the CLEANING of the cooling system. Your shop fails to understand that coolant passes through the egr and with the presence of oil it wouldn't be long for this world to operate it like that.
HNC Medium And Heavy Duty Truck Parts Online | Ford Water Pumps & Cooling System : VT365 Oil Cooler Kit 1886511C93
The above is just one of many parts houses that supplies coolers. Like I said these things are pretty cheap, they are also common failure points of these trucks, The bulletproof fix is the sinister diesel external oil cooler with adapter plate. I personally wouldn't run it because then you lose the ability to warm the oil up with coolant temperature when the engine is cold. (being that you live in idaho that is kind of important if your also running a block heater)