Mechanically there is no difference in the pumps. There are various versions of the long pump with different bosses drilled, tapped etc. for specific applications. And, proper matching pulleys must be used.
I had a 40 Std. Ford Coupe with 350 and short pump, but converted to long pump and appropriate pulley system. There was no problem in radiator clearance, in fact the long pump is less than 1" longer than the short and the fan actually fit closer to specs with the long pump.
After making sure I had no air leaks over, under, and to the sides of the radiator I had no heating problems ever again in the '40.