You can make changes, but they need to be within original equipment specs.
This may help:
For flares - need to cover the top of the tire and extend to or past the horizontal plane of the tire. They cannot be extended (2 piece) to go past the plane, need to be a one piece. Also note the reference to flaps if flares are "impractical".
For bumper - depends on the class of the car, so either 20" or 28" (likely 28 for a jeep) from road to bottom of the bumper - again, looks like it needs to be one piece or you'll likely fail.
State vehicle inspection requirements are state laws only they are not criminal misdemeanors or felony offenses. - this is why a police officer can pull you over and give you a citation for a brake light or the infamous license plate light being out.