Do you have a new timing chain cover, by chance? Might be the holes for the fuel pump mount are offset toward the engine a bit, bringing the pump arm into contact with the chain? Or, the plate that is used for the tensioner is thicker than original plate, and doesn't let cam sit back against rear plug when gear is on cam. Did you have new cam plug installed on back of engine, and set too deep when installed (holds cam forward slightly, causing it to rub).
Ideal world, things should not change with modification you did and affect pump arm rubbing...
If cam is in wrong position, it will have lifters offset on cam lobes as well...