It is hard to determine what is causing your clearance problem without seeing photos of the radiator and water pump and fan blade. But, if the extra thickness of the radiator is on the engine side of the radiator housing/frame, yes, that would result in the radiator being closer to the fan.
Not knowing what mounting frame you have, no one can tell you if need to get a different mounting frame for correct installation of a 3100 radiator.
