I would want to compare the old pump shaft angle to the new shaft pump angle. Where the fuel pump rod hits.
If the 350 one is say 20 more degrees then the other that is going to place additional wear on the fuel pump cam lobe. If the 350 one's angle was less then the old pump then the plunger wont be pushed down completely making the pump work harder to maintain pressure.
Now you can fix this. You just need to adjust the length of the rod after a bit of checking/math.
If they are both the same angle then your good to run it. The engine will not care as long as the fuel pressures are the same.