I wonder if there could be anything on the airside? Is it a turbo unit? If so, I wonder if there could be a leak (crack?) in any of the turbo pipes or connections? That can happen from time to time -- it screws up the air/fuel regulation, sucks air from the wrong place. If it is a turbo unit, I've check turbos on other rigs by removing the hose/pipe ends , blocking off with a PVC pipe caps and hose clamps ....and screw a spray paint gun regulator into one of the PVC caps so I could apply 10 psi on the system and listen for air leaks (I've found a few in the past, and at other times ruled out any turbo leaks).
Also as another thought, I don't know if your skid steer has a snow or bug screen on the air intake before or after the air filter, but I've seen them on other diesel rigs where there's a fine mesh screen in the intake pipe. They can become partially plugged up if a leaf or some bugs get in there. The added resistance can screw up the airflow. It's a bugger but the screens, when they exist, can be hidden and you'd never know they existed if ya didn't remove the air intake system and look into the air intake pipes. Not saying your Case has a screen, but just trying to throw out ideas if the fuel ideas others have thrown out don't fix things. Maybe others can chime in who know the machine a little better, or you could drop by your dealer and ask a mechanic.
Let us know what you find.