The Sunbelt guy may have been a bit optimistic. The skid steer (Bobcat S550?) weighs about 6200 lbs. Add another 900 for the grapple, maybe 1200 for the tree shear, and let's say 3500 for the equipment trailer. Not a lot of aerodynamic drag, but weight in the hills.
The holes in the skid plate have to help, but if you are still getting codes, I'd be looking at the shrouds ahead of the intercooler. On the stock truck, there are no gaps between the cutouts in the bumper and the intercooler itself. Just trying to snake a block heater cord into that opening is a job. I suspect that plastic "shield" under the engine is primarily to direct cooling air where it belongs as well. Beyond that, I would convert the holes in your skid plate to NACA ducts. Let us know if the holes alone addressed the issue.